From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 1 14:57:24 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j01KvORV004381 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 1 Jan 2005 14:57:24 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j01KvNTv004380 for namd-l-outgoing; Sat, 1 Jan 2005 14:57:23 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from trend1.tcs.tulane.edu (trend1-vw.tcs.tulane.edu [129.81.255.235]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j01KurRU004351; Sat, 1 Jan 2005 14:56:54 -0600 (CST) Received: from trend1.tcs.tulane.edu (localhost [127.0.0.1]) by trend1.tcs.tulane.edu (8.12.10/8.12.8) with ESMTP id j01KumMk027321; Sat, 1 Jan 2005 14:56:48 -0600 Received: from tulane.edu (treat.tcs.tulane.edu [129.81.224.58]) by trend1.tcs.tulane.edu (8.12.10/8.12.10) with ESMTP id j01KumiY027315; Sat, 1 Jan 2005 14:56:48 -0600 Received: from localhost (rsalmon@localhost) by tulane.edu (8.12.8/8.12.8/Submit) with ESMTP id j01Kuugt016989; Sat, 1 Jan 2005 14:56:56 -0600 Date: Sat, 1 Jan 2005 14:56:56 -0600 (CST) From: Rene Salmon X-X-Sender: rsalmon@treat.tcs.tulane.edu To: Gengbin Zheng cc: namd-l@ks.uiuc.edu Subject: Re: namd-l: clustermatic 4 and 5 Namd/charm In-Reply-To: <41D59609.3090704@ks.uiuc.edu> Message-ID: References: <41D4A2DF.7060307@ks.uiuc.edu> <41D59609.3090704@ks.uiuc.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, The problem with charm was indeed the missing libs on the slave nodes. After I added the missing libs the charm tests worked fine. Next I moved to compile NAMD. I just followed your instructions and copied the "Linux-i686-Clustermatic.arch" to "Linux-amd64-Clustermatic.arch" here is what the file looks like: NAMD_2.5_Source/arch# cat Linux-amd64-Clustermatic.arch include .rootdir/arch/Linux-amd64-g++.arch CHARMARCH = net-linux-amd64-clustermatic -------- here is what Linux-amd64-g++.arch looks like: NAMD_2.5_Source/arch# cat Linux-amd64-g++.arch NAMD_ARCH = Linux-amd64 CHARMARCH = net-linux-amd64-clustermatic CXX = g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H CXXOPTS = -O3 -fexpensive-optimizations -ffast-math CC = gcc COPTS = -O3 -fexpensive-optimizations -ffast-math ----------------------- Next I tried to configure and compile: NAMD_2.5_Source/arch# ./config Linux-amd64-Clustermatic this worked and generated the NAMD executables with out any errors. I ran this test on NAMD: ./charmrun ++skipmaster ++verbose ++startpe 0 +p2 ./namd2 /tmp/alanin WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 9 WRITING COORDINATES TO OUTPUT FILE AT STEP 9 WRITING VELOCITIES TO OUTPUT FILE AT STEP 9 ========================================== WallClock: 1.611247 CPUTime: 1.201816 Memory: 8895 kB Charmrun> Graceful exit. It seems to be working fine. Thank you very much for getting me this far. ---------------------- I would like to have the fftw libs with NAMD so I tried this: NAMD_2.5_Source/arch# ./config tcl fftw Linux-amd64-Clustermatic If I add the fftw or tcl or both I get error messages and I do not get a NAMD binary. I installed fftw-3.0.1 from the fftw website with out any problems and just pointed the Linux-amd64.fftw to the fftw install. I also have tcl-8.4 installed on the system and I edited the Linux-amd64.tcl file to reflect the location of the libs and include files for tcl. Is there anything special I need to do to get NAMD to compile with fftw support? I checked the NAMD www site for precompiled libraries for both tcl and fftw for amd64 but found nothing. Anyone have these libs precompiled to work with NAMD? Thank you very much for all the help Rene From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 1 15:15:52 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j01LFqRV004996 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 1 Jan 2005 15:15:52 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j01LFqVk004995 for namd-l-outgoing; Sat, 1 Jan 2005 15:15:52 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from sccimhc91.asp.att.net (sccimhc91.asp.att.net [63.240.76.165]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j01LFpRU004986 for ; Sat, 1 Jan 2005 15:15:51 -0600 (CST) Received: from [192.168.2.5] (12-221-89-211.client.insightbb.com[12.221.89.211]) by sccimhc91.asp.att.net (sccimhc91) with ESMTP id <20050101211545i9100rfol0e>; Sat, 1 Jan 2005 21:15:45 +0000 Message-ID: <41D71301.5050105@ks.uiuc.edu> Date: Sat, 01 Jan 2005 15:15:45 -0600 From: Gengbin Zheng User-Agent: Mozilla Thunderbird 0.9 (Windows/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Rene Salmon CC: namd-l@ks.uiuc.edu Subject: Re: namd-l: clustermatic 4 and 5 Namd/charm References: <41D4A2DF.7060307@ks.uiuc.edu> <41D59609.3090704@ks.uiuc.edu> In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi Rene, Good to hear Charm++ and NAMD runs on opteron with clustermatic 5. For fftw support, you need to download fftw version 2 instead of version 3 in order to compile NAMD. And you need to compile tcl in its static form (.a) instead of shared lib for NAMD. For detailed instruction on how to configure and compile it, please see my NAMD wiki at http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile Alternatively, I think there are binaries on NAMD website you can download for the fftw and tcl precompiled for opteron. Gengbin Rene Salmon wrote: > > > Hi, > > The problem with charm was indeed the missing libs on the slave nodes. > After I added the missing libs the charm tests worked fine. > > Next I moved to compile NAMD. I just followed your instructions and > copied the "Linux-i686-Clustermatic.arch" to > "Linux-amd64-Clustermatic.arch" here is what the file looks like: > > NAMD_2.5_Source/arch# cat Linux-amd64-Clustermatic.arch > include .rootdir/arch/Linux-amd64-g++.arch > > CHARMARCH = net-linux-amd64-clustermatic > > > -------- > here is what Linux-amd64-g++.arch looks like: > > NAMD_2.5_Source/arch# cat Linux-amd64-g++.arch > NAMD_ARCH = Linux-amd64 > CHARMARCH = net-linux-amd64-clustermatic > > CXX = g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H > CXXOPTS = -O3 -fexpensive-optimizations -ffast-math > CC = gcc > COPTS = -O3 -fexpensive-optimizations -ffast-math > > > > ----------------------- > > Next I tried to configure and compile: > > NAMD_2.5_Source/arch# ./config Linux-amd64-Clustermatic > > this worked and generated the NAMD executables with out any errors. > I ran this test on NAMD: > > ./charmrun ++skipmaster ++verbose ++startpe 0 +p2 ./namd2 /tmp/alanin > > WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 9 > WRITING COORDINATES TO OUTPUT FILE AT STEP 9 > WRITING VELOCITIES TO OUTPUT FILE AT STEP 9 > ========================================== > WallClock: 1.611247 CPUTime: 1.201816 Memory: 8895 kB > Charmrun> Graceful exit. > > > It seems to be working fine. Thank you very much for getting me this > far. > > > > > ---------------------- > I would like to have the fftw libs with NAMD so I tried this: > > NAMD_2.5_Source/arch# ./config tcl fftw Linux-amd64-Clustermatic > > If I add the fftw or tcl or both I get error messages and I do not get > a NAMD binary. > > I installed fftw-3.0.1 from the fftw website with out any problems and > just pointed the Linux-amd64.fftw to the fftw install. > > I also have tcl-8.4 installed on the system and I edited the > Linux-amd64.tcl file to reflect the location of the libs and include > files for tcl. > > > Is there anything special I need to do to get NAMD to compile with > fftw support? I checked the NAMD www site for precompiled libraries > for both tcl and fftw for amd64 but found nothing. Anyone have these > libs precompiled to work with NAMD? > > Thank you very much for all the help > > Rene > > > > > > > > > > From owner-namd-l@halifax.ks.uiuc.edu Sun Jan 2 02:01:40 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0281eRV018909 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sun, 2 Jan 2005 02:01:40 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0281eYf018907 for namd-l-outgoing; Sun, 2 Jan 2005 02:01:40 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from web40808.mail.yahoo.com (web40808.mail.yahoo.com [66.218.78.185]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with SMTP id j0281cRU018882 for ; Sun, 2 Jan 2005 02:01:39 -0600 (CST) Received: (qmail 84198 invoked by uid 60001); 2 Jan 2005 08:01:32 -0000 Message-ID: <20050102080132.84196.qmail@web40808.mail.yahoo.com> Received: from [202.114.78.142] by web40808.mail.yahoo.com via HTTP; Sun, 02 Jan 2005 16:01:32 CST Date: Sun, 2 Jan 2005 16:01:32 +0800 (CST) From: =?gb2312?q?=CD=F5=D0=A1=C7=E5?= Subject: namd-l: About charm++/namd on AMD64 cluster To: namd-l@ks.uiuc.edu MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Dear all, I builded the net version of charm++/namd on AMD64 cluster.But when i test the command "charmrun hello" the error is "ERROR>Cannot obtain IP address of localhost". If i only use "namd2 " the error "segmentation fault" appears after fftw is done. Why they cannot work ? Should i compile "mpi" version of charm++? Thanks! Xiaoqing,Wang Wuhan University Whuhan,China _________________________________________________________ Do You Yahoo!? 注册世界一流品质的雅虎免费电邮 http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/ From owner-namd-l@halifax.ks.uiuc.edu Sun Jan 2 02:51:03 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j028p3RV019791 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sun, 2 Jan 2005 02:51:03 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j028p3qT019790 for namd-l-outgoing; Sun, 2 Jan 2005 02:51:03 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from sccimhc91.asp.att.net (sccimhc91.asp.att.net [63.240.76.165]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j028p2RU019785 for ; Sun, 2 Jan 2005 02:51:02 -0600 (CST) Received: from [192.168.2.5] (12-221-89-211.client.insightbb.com[12.221.89.211]) by sccimhc91.asp.att.net (sccimhc91) with ESMTP id <20050102085057i9100rfneie>; Sun, 2 Jan 2005 08:50:57 +0000 Message-ID: <41D7B5F0.9060407@ks.uiuc.edu> Date: Sun, 02 Jan 2005 02:50:56 -0600 From: Gengbin Zheng User-Agent: Mozilla Thunderbird 0.9 (Windows/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: =?GB2312?B?zfXQocfl?= CC: namd-l@ks.uiuc.edu Subject: Re: namd-l: About charm++/namd on AMD64 cluster References: <20050102080132.84196.qmail@web40808.mail.yahoo.com> In-Reply-To: <20050102080132.84196.qmail@web40808.mail.yahoo.com> Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: 8bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, Could you please tell us how did you compile Charm++ and NAMD? For parallel run case, you need to write a nodelist file which normally should not contain localhost. But specifically for your case, I bet you don't have an entry in /etc/hosts for localhost, and so localhost is not able to be resolved to the IP address of 127.0.0.1. Try command "ping localhost" and see what happens. Gengbin 王小清 wrote: >Dear all, > I builded the net version of charm++/namd on AMD64 >cluster.But when i test the command "charmrun hello" >the error is "ERROR>Cannot obtain IP address of >localhost". >If i only use "namd2 " the error >"segmentation fault" appears after fftw is done. > Why they cannot work ? > Should i compile "mpi" version of charm++? > >Thanks! > > >Xiaoqing,Wang >Wuhan University >Whuhan,China > >_________________________________________________________ >Do You Yahoo!? >注册世界一流品质的雅虎免费电邮 >http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/ > > From owner-namd-l@halifax.ks.uiuc.edu Sun Jan 2 14:19:12 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j02KJCRV007088 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sun, 2 Jan 2005 14:19:12 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j02KJCwm007087 for namd-l-outgoing; Sun, 2 Jan 2005 14:19:12 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from sccrmhc13.comcast.net (sccrmhc13.comcast.net [204.127.202.64]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j02KIoRU007068; Sun, 2 Jan 2005 14:18:50 -0600 (CST) Received: from [192.168.0.103] (c-24-16-39-253.client.comcast.net[24.16.39.253]) by comcast.net (sccrmhc13) with ESMTP id <2005010220182501600ppki0e>; Sun, 2 Jan 2005 20:18:26 +0000 Message-ID: <41D85717.3020606@whimsey.com> Date: Sun, 02 Jan 2005 12:18:31 -0800 From: John Saeger User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Gengbin Zheng CC: namd-l@ks.uiuc.edu Subject: Re: namd-l: clustermatic 4 and 5 Namd/charm References: <41D4A2DF.7060307@ks.uiuc.edu> <41D59609.3090704@ks.uiuc.edu> <41D71301.5050105@ks.uiuc.edu> In-Reply-To: <41D71301.5050105@ks.uiuc.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk It's a wonderful world. Almost magical at times. This is exactly what I'm looking for. Would it be possible for somebody to put a binary of this somewhere so I could try it out? BTW, now that I know about CVS and Wiki, I may give compiling another chance, but in the meantime, binaries are very helpful. Maybe you should have some *bleeding edge* binaries to go along with CVS? Thanks! John Gengbin Zheng wrote: > > Hi Rene, > > Good to hear Charm++ and NAMD runs on opteron with clustermatic 5. > > For fftw support, you need to download fftw version 2 instead of version > 3 in order to compile NAMD. > And you need to compile tcl in its static form (.a) instead of shared > lib for NAMD. > For detailed instruction on how to configure and compile it, please see > my NAMD wiki at > http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile > > Alternatively, I think there are binaries on NAMD website you can > download for the fftw and tcl precompiled for opteron. > > Gengbin > > Rene Salmon wrote: > >> >> >> Hi, >> >> The problem with charm was indeed the missing libs on the slave nodes. >> After I added the missing libs the charm tests worked fine. >> >> Next I moved to compile NAMD. I just followed your instructions and >> copied the "Linux-i686-Clustermatic.arch" to >> "Linux-amd64-Clustermatic.arch" here is what the file looks like: >> >> NAMD_2.5_Source/arch# cat Linux-amd64-Clustermatic.arch >> include .rootdir/arch/Linux-amd64-g++.arch >> >> CHARMARCH = net-linux-amd64-clustermatic >> >> >> -------- >> here is what Linux-amd64-g++.arch looks like: >> >> NAMD_2.5_Source/arch# cat Linux-amd64-g++.arch >> NAMD_ARCH = Linux-amd64 >> CHARMARCH = net-linux-amd64-clustermatic >> >> CXX = g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H >> CXXOPTS = -O3 -fexpensive-optimizations -ffast-math >> CC = gcc >> COPTS = -O3 -fexpensive-optimizations -ffast-math >> >> >> >> ----------------------- >> >> Next I tried to configure and compile: >> >> NAMD_2.5_Source/arch# ./config Linux-amd64-Clustermatic >> >> this worked and generated the NAMD executables with out any errors. >> I ran this test on NAMD: >> >> ./charmrun ++skipmaster ++verbose ++startpe 0 +p2 ./namd2 /tmp/alanin >> >> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 9 >> WRITING COORDINATES TO OUTPUT FILE AT STEP 9 >> WRITING VELOCITIES TO OUTPUT FILE AT STEP 9 >> ========================================== >> WallClock: 1.611247 CPUTime: 1.201816 Memory: 8895 kB >> Charmrun> Graceful exit. >> >> >> It seems to be working fine. Thank you very much for getting me this >> far. >> >> >> >> >> ---------------------- >> I would like to have the fftw libs with NAMD so I tried this: >> >> NAMD_2.5_Source/arch# ./config tcl fftw Linux-amd64-Clustermatic >> >> If I add the fftw or tcl or both I get error messages and I do not get >> a NAMD binary. >> >> I installed fftw-3.0.1 from the fftw website with out any problems and >> just pointed the Linux-amd64.fftw to the fftw install. >> >> I also have tcl-8.4 installed on the system and I edited the >> Linux-amd64.tcl file to reflect the location of the libs and include >> files for tcl. >> >> >> Is there anything special I need to do to get NAMD to compile with >> fftw support? I checked the NAMD www site for precompiled libraries >> for both tcl and fftw for amd64 but found nothing. Anyone have these >> libs precompiled to work with NAMD? >> >> Thank you very much for all the help >> >> Rene >> >> >> >> >> >> >> >> >> >> > > From owner-namd-l@halifax.ks.uiuc.edu Sun Jan 2 15:35:45 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j02LZjRV009391 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sun, 2 Jan 2005 15:35:45 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j02LZjP8009390 for namd-l-outgoing; Sun, 2 Jan 2005 15:35:45 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from smtpvip1.bnl.gov (smtp@smtpgateway.BNL.GOV [130.199.3.132]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j02LZiRU009386 for ; Sun, 2 Jan 2005 15:35:44 -0600 (CST) Received: from exchange10.b459.bnl.gov ([130.199.74.42] helo=exchange10.bnl.gov) by smtpvip1.bnl.gov with esmtp (bnl.gov SMTP) id 1ClDO6-0006LT-00 for ; Sun, 02 Jan 2005 16:35:46 -0500 Received: by exchange10.b459.bnl.gov with Internet Mail Service (5.5.2657.72) id ; Sun, 2 Jan 2005 16:35:43 -0500 Message-ID: <47B8E77FE2707145932EADD8C529D77F01CD02EA@exchange10.b459.bnl.gov> From: "Stern, Julie" To: "'namd-l@ks.uiuc.edu'" Subject: namd-l: prmtop reading error Date: Sun, 2 Jan 2005 16:35:42 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain X-BNL-MailScanner-Information: Please contact the ITD Service Desk for more information X-BNL-MailScanner: Found to be clean X-BNL-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=0, required 5, autolearn=disabled) X-MailScanner-From: jvstern@bnl.gov Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hello, I ran namd on Lemieux for the very first time and got the following error: Info: Using AMBER format force field! Info: AMBER PARM FILE subtest.prmtop Info: Exclusions in PARM file will be ignored! Reading parm file (subtest.prmtop) ... not equipped to read perturbation prmtop FATAL ERROR: Failed to read AMBER parm file! Since my programs worked with my local version of NAMD, does anyone know what is wrong with my prmtop file and what do they mean by 'perturbation prmtop'? Thanks. Julie From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 3 04:15:27 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j03AFRRV029388 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 3 Jan 2005 04:15:27 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j03AFR3c029387 for namd-l-outgoing; Mon, 3 Jan 2005 04:15:27 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from web40810.mail.yahoo.com (web40810.mail.yahoo.com [66.218.78.187]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with SMTP id j03AFPRU029378 for ; Mon, 3 Jan 2005 04:15:26 -0600 (CST) Received: (qmail 65980 invoked by uid 60001); 3 Jan 2005 10:15:19 -0000 Message-ID: <20050103101519.65978.qmail@web40810.mail.yahoo.com> Received: from [202.114.78.142] by web40810.mail.yahoo.com via HTTP; Mon, 03 Jan 2005 18:15:19 CST Date: Mon, 3 Jan 2005 18:15:19 +0800 (CST) From: =?gb2312?q?=CD=F5=D0=A1=C7=E5?= Subject: Re: namd-l: About charm++/namd on AMD64 cluster To: namd-l@ks.uiuc.edu In-Reply-To: <41D8370B.2060208@ks.uiuc.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi I downloaded the latest Charm++ and compiled the mpi version of Charm++/NAMD on amd64 cluster.They can work now.Thanks! I made a simple 100 steps minimization.But why the CPUTime is become longer with increasing the number of cpus?What factors affect the CPUTime? Thanks in advance! --- Gengbin Zheng 的正文： > > This errors should be fine as they are fortran > related and NAMD does not > written in fortran. > Have you tried test program in > charm/pgms/charm++/megatest? Whatis the > result? > If it fails, Maybe you should download the latest > source from Charm++ > website. > > Gengbin > _________________________________________________________ Do You Yahoo!? 注册世界一流品质的雅虎免费电邮 http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/ From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 3 14:47:07 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j03Kl7RV026488 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 3 Jan 2005 14:47:07 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j03Kl7Zb026487 for namd-l-outgoing; Mon, 3 Jan 2005 14:47:07 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from sccimhc91.asp.att.net (sccimhc91.asp.att.net [63.240.76.165]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j03Kl6RU026482 for ; Mon, 3 Jan 2005 14:47:06 -0600 (CST) Received: from [192.168.2.5] (12-221-89-211.client.insightbb.com[12.221.89.211]) by sccimhc91.asp.att.net (sccimhc91) with ESMTP id <20050103204700i9100rfha8e>; Mon, 3 Jan 2005 20:47:01 +0000 Message-ID: <41D9AF42.8000804@ks.uiuc.edu> Date: Mon, 03 Jan 2005 14:46:58 -0600 From: Gengbin Zheng User-Agent: Mozilla Thunderbird 0.9 (Windows/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: =?GB2312?B?zfXQocfl?= CC: namd-l@ks.uiuc.edu Subject: Re: namd-l: About charm++/namd on AMD64 cluster References: <20050103101519.65978.qmail@web40810.mail.yahoo.com> In-Reply-To: <20050103101519.65978.qmail@web40810.mail.yahoo.com> Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: 8bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, Adding CPUs sure can slow down program if 1. your atom system is too small, and then imaging more people do one trivial task can be slower than just one man do the same task alone due to the synchronization overhead. 2. The communication hardware is slow, for example 100Mbps ethernet is inefficient especially for small job. In which case, there is not enough computation work to overlap the communication latency. so try some larger system for example apoa1 benchmark (you can download it from NAMD website) and see how it scales. Gengbin 王小清 wrote: >Hi > I downloaded the latest Charm++ and compiled the mpi >version of Charm++/NAMD on amd64 cluster.They can work >now.Thanks! > I made a simple 100 steps minimization.But why the >CPUTime is become longer with increasing the number of >cpus?What factors affect the CPUTime? > >Thanks in advance! > > --- Gengbin Zheng 的正文： > > >>This errors should be fine as they are fortran >>related and NAMD does not >>written in fortran. >>Have you tried test program in >>charm/pgms/charm++/megatest? Whatis the >>result? >>If it fails, Maybe you should download the latest >>source from Charm++ >>website. >> >>Gengbin >> >> >> > > >_________________________________________________________ >Do You Yahoo!? >注册世界一流品质的雅虎免费电邮 >http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/ > > From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 3 17:48:37 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j03NmbRV008601 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 3 Jan 2005 17:48:37 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j03Nmbus008600 for namd-l-outgoing; Mon, 3 Jan 2005 17:48:37 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from cancun.ks.uiuc.edu (cancun.ks.uiuc.edu [130.126.120.136]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j03NmaRU008596 for ; Mon, 3 Jan 2005 17:48:36 -0600 (CST) Received: (from jim@localhost) by cancun.ks.uiuc.edu (8.12.10+Sun/8.12.10/Submit) id j03NmaXm007094 for namd-l@ks.uiuc.edu; Mon, 3 Jan 2005 17:48:36 -0600 (CST) Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.195]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j03NRpRU007756 for ; Mon, 3 Jan 2005 17:27:51 -0600 (CST) Received: by wproxy.gmail.com with SMTP id 70so234577wra for ; Mon, 03 Jan 2005 15:27:46 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding; b=KrhmEaq9Bncf02vCCHru/ODOxgq4IVCv/P5GBRfALoFivKTrnKREeAH3Vn9+8oW14jT4QzNhqGaP0DSHRUbN2qAK+Lu4S0MZqUID8zsWwzv5yhIO/oJdeLMtcYSbTa4D7r5ohW3tNoVcJ/RWbXcF0HaVqn9ni7t3hBWj6pyYdJY= Received: by 10.54.23.71 with SMTP id 71mr207067wrw; Mon, 03 Jan 2005 15:27:45 -0800 (PST) Received: by 10.54.30.54 with HTTP; Mon, 3 Jan 2005 15:27:45 -0800 (PST) Message-ID: <92be0d4505010315275f90db99@mail.gmail.com> Date: Mon, 3 Jan 2005 18:27:45 -0500 From: Peter Bazeley Reply-To: Peter Bazeley To: NAMD Subject: namd-l: increase in energy over time Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hello I am simulating a protein with NAMD, using a basic set of parameters. I minimize my protein for 1000 timesteps, then run for 50000 timesteps. I've found that the TOTAL energy of the system increases over time. I guess I'm trying to figure out the reason behind this. Could it be that I am seeing the entropic effects on the protein over time? Or perhaps the minimization created a structure that is lower in energy than would be expected in vivo, and the simulation brings the structure back to a more normal state? Thanks for any input, Peter Bazeley From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 3 18:29:51 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j040TpRV009856 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 3 Jan 2005 18:29:51 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j040Tpme009855 for namd-l-outgoing; Mon, 3 Jan 2005 18:29:51 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from ipstpost.umd.edu (IDENT:root@ipstpost.umd.edu [129.2.9.228]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j040ToRU009850 for ; Mon, 3 Jan 2005 18:29:50 -0600 (CST) Received: from lakers.umd.edu (sendmail@lakers.umd.edu [128.8.92.100]) by ipstpost.umd.edu (8.12.10/8.12.10) with ESMTP id j040Tl42023826; Mon, 3 Jan 2005 19:29:47 -0500 (EST) Received: from localhost (edobrien@localhost) by lakers.umd.edu (8.12.10/8.12.10) with ESMTP id j040Tk48013357; Mon, 3 Jan 2005 19:29:46 -0500 (EST) X-Authentication-Warning: lakers.umd.edu: edobrien owned process doing -bs Date: Mon, 3 Jan 2005 19:29:46 -0500 (EST) From: Edward Patrick Obrien X-X-Sender: edobrien@lakers.umd.edu To: Peter Bazeley cc: NAMD Subject: Re: namd-l: increase in energy over time In-Reply-To: <92be0d4505010315275f90db99@mail.gmail.com> Message-ID: References: <92be0d4505010315275f90db99@mail.gmail.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi Peter, In the microconanical ensemble (NVE) energy drift (change in total energy as a function of time) occurs due to finite integration errors associated with discretizing newton's equations of motion. Typically the total kinetic energy becomes more positive correlating with an increase in temperature. You should check these two quantities, and see if they are increasing. If you are running in the canonical (NVT) or Gibbs (NPT) ensemble your total energy should fluctuate. You want to avoid energy drift in NVE because it is non-physical, and can mess up your dynamics. To minimize energy drift make sure your system is well minimized (Gradient tolerance < 1.0 or less), heat your sytem in steps (I typically due it over the course of 300 ps) to the temperature desired, and use a reasonable time integration step (conventionally 1 fs at 300K). I don't believe you are seeing entropic effect, as the energy you are probably looking at is the energy of the system (which neglects the entropic term) and not the free energy. The minimization step is equivalent to carrying out a simulation at temperature equal to 0 K, because the motion is determine only by the gradient of the potential energy, and there is no kinetic term. Thus, if you did not heat your system up properly, I believe jumping the temperature from 0K up to 300 K could lead to bad van der Walls interactions, which would cause your energy to drift. Hope that helps, Ed On Mon, 3 Jan 2005, Peter Bazeley wrote: > Hello > > I am simulating a protein with NAMD, using a basic set of parameters. > I minimize my protein for 1000 timesteps, then run for 50000 > timesteps. I've found that the TOTAL energy of the system increases > over time. I guess I'm trying to figure out the reason behind this. > Could it be that I am seeing the entropic effects on the protein over > time? Or perhaps the minimization created a structure that is lower in > energy than would be expected in vivo, and the simulation brings the > structure back to a more normal state? > > Thanks for any input, > Peter Bazeley > From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 4 01:13:44 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j047DiRV019663 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 4 Jan 2005 01:13:44 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j047DiXl019662 for namd-l-outgoing; Tue, 4 Jan 2005 01:13:44 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from web40627.mail.yahoo.com (web40627.mail.yahoo.com [66.218.92.56]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with SMTP id j047DhRU019658 for ; Tue, 4 Jan 2005 01:13:43 -0600 (CST) Received: (qmail 17834 invoked by uid 60001); 4 Jan 2005 07:13:37 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=nO+QDVdUmyyymWahuhAgEBHpDlxkuc1PXDFvQm5vA4C5rDKHbg0QpMJIM5BJXnO48DME3n8ggLzS5ool+dJy6QqQWwuynI9wirslbQTvsVFQ44LRLG0YQsdpxJHpwcb9oQig1urbkcGyG49bAstxdcOVCv9YKb3vCS+24tNBdO0= ; Message-ID: <20050104071337.17832.qmail@web40627.mail.yahoo.com> Received: from [193.140.61.102] by web40627.mail.yahoo.com via HTTP; Mon, 03 Jan 2005 23:13:37 PST Date: Mon, 3 Jan 2005 23:13:37 -0800 (PST) From: bora erdemli Subject: Re: namd-l: Bug alert!!! To: Ioana Cozmuta , namd-l@ks.uiuc.edu In-Reply-To: <66f16fbb0412240647d5b2d35@mail.gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Dear All; I need help about the following error occured during simulation. Processor 0 Exiting: Called CmiAbort Reason: BUG ALERT: Stray PME grid charges detected! BUG ALERT: NAMD has detected a bug. Please notify namd@ks.uiuc.edu. req_handle_abort called Fatal error on PE 0> BUG ALERT: Stray PME grid charges detected! BUG ALERT: NAMD has detected a bug. Please notify namd@ks.uiuc.edu. I could visualize my system and everything seems to be ok . I have some free charges around my system which I did put them by using VMD autoionize plug-in in order to neutralize the system. I made 10000 minimization by using usual NAMD procedure no simulated annealing or such modification. --- Ioana Cozmuta wrote: > Did you vizualize your trajectory? Do you have free > charges > (counterions) around your system? What system are > you looking at? What > was your equilibration procedure? Do you see the > system splitting > > If you give more information I might be able to help > if none else has > a better idea. > > Ioana > > > -- > Ioana Cozmuta, Ph.D. > Eloret Corporation > NASA Ames Research Center > http://people.nas.nasa.gov/~ioana/ > w (650) 604-0993, h (408) 732-1399 > On Thu, 23 Dec 2004 23:06:32 -0800 (PST), bora > erdemli > wrote: > > > > Dear All; > > > > After almost 2 ns simulation , I faced with the > > following error and my simulation was stopped. > > What could be the reason? > > > > best regards.... > > > > ------------ Processor 0 Exiting: Called CmiAbort > > ------------ > > Reason: BUG ALERT: Stray PME grid charges > detected! > > > > BUG ALERT: NAMD has detected a bug. Please notify > > namd@ks.uiuc.edu. > > > > req_handle_abort called > > Fatal error on PE 0> BUG ALERT: Stray PME grid > charges > > detected! > > > > BUG ALERT: NAMD has detected a bug. Please notify > > namd@ks.uiuc.edu. > > > > ===== > > Sabri Bora Erdemli > > Koc University > > Computational Science and Engineering > > Research and Teaching Asistant > > Koc Universitesi pk.218 34550 > > sariyer Istanbul/TURKEY > > tel no: 02123381736 > > 05326512523 > > > > > > __________________________________ > > Do you Yahoo!? > > Yahoo! Mail - You care about security. So do we. > > http://promotions.yahoo.com/new_mail > > > ===== Sabri Bora Erdemli Koc University Computational Science and Engineering Research and Teaching Asistant Koc Universitesi pk.218 34550 sariyer Istanbul/TURKEY tel no: 02123381736 05326512523 __________________________________ Do you Yahoo!? Send a seasonal email greeting and help others. Do good. http://celebrity.mail.yahoo.com From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 4 10:13:43 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j04GDhRV005659 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 4 Jan 2005 10:13:43 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j04GDh1H005658 for namd-l-outgoing; Tue, 4 Jan 2005 10:13:43 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from cancun.ks.uiuc.edu (cancun.ks.uiuc.edu [130.126.120.136]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j04GDgRU005654 for ; Tue, 4 Jan 2005 10:13:42 -0600 (CST) Received: (from jim@localhost) by cancun.ks.uiuc.edu (8.12.10+Sun/8.12.10/Submit) id j04GDgeh007398 for namd-l@ks.uiuc.edu; Tue, 4 Jan 2005 10:13:42 -0600 (CST) Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.207]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j043JdRU014225 for ; Mon, 3 Jan 2005 21:19:39 -0600 (CST) Received: by wproxy.gmail.com with SMTP id 70so271952wra for ; Mon, 03 Jan 2005 19:19:33 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:references; b=oPgAfSaJfIzgMybV5OM6AZyMTLUZCWI8OHbSFUDkNEo6ZROHzP3LHCWI8rGyeNXy6Nl94mIzQ5xCGqq1aP/FrzOywU+6o42KOY7Xr395Sm2ARaru3jIkpK4vowIJlYTz7Bn4YvncBrUCE56P/oTDSybt8O4Wqk9KDXvSoxNMJAs= Received: by 10.54.36.27 with SMTP id j27mr15728wrj; Mon, 03 Jan 2005 19:19:33 -0800 (PST) Received: by 10.54.30.54 with HTTP; Mon, 3 Jan 2005 19:19:33 -0800 (PST) Message-ID: <92be0d4505010319196b360505@mail.gmail.com> Date: Mon, 3 Jan 2005 22:19:33 -0500 From: Peter Bazeley Reply-To: Peter Bazeley To: Edward Patrick Obrien Subject: Re: namd-l: increase in energy over time Cc: NAMD In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit References: <92be0d4505010315275f90db99@mail.gmail.com> Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi Ed Thanks for your response. You are right in that there is a gradual rise in both temperature and kinetic energy, which corresponds to the rise in total energy. My total simulation time is only 100 ps, so I imagine that jumping from a temperature of 0 to 300 would have a significant effect. I know that in a simple force field equation, potential energy is the sum of the bond, angle, improper, dihedral, electrostatic, and VDW energies. Do you know if the boundary and miscellaneous energies get added to that as well? It seems that 300K is a very common temperature in NAMD runs, yet physiological conditions are closer to 310K. Do you know why 300 is preferred? Thanks again, Peter Bazeley On Mon, 3 Jan 2005 19:29:46 -0500 (EST), Edward Patrick Obrien wrote: > Hi Peter, > In the microconanical ensemble (NVE) energy drift (change in total > energy as a function of time) occurs due to finite integration errors > associated with discretizing newton's equations of motion. > Typically the total kinetic energy becomes more positive correlating with > an increase in temperature. You should check these two quantities, and see > if they are increasing. > > If you are running in the canonical (NVT) or Gibbs (NPT) ensemble your > total energy should fluctuate. > > You want to avoid energy drift in NVE because it is non-physical, and > can mess up your dynamics. > > To minimize energy drift make sure your system is well minimized > (Gradient tolerance < 1.0 or less), heat your sytem in steps (I typically > due it over the course of 300 ps) to the > temperature desired, and use a reasonable time integration step > (conventionally 1 fs at 300K). > > I don't believe you are seeing entropic effect, as the energy you are > probably looking at is the energy of the system (which neglects the > entropic term) and not the free energy. > > The minimization step is equivalent to carrying out a simulation at > temperature equal to 0 K, because the motion is determine only by the > gradient of the potential energy, and there is no kinetic term. Thus, if > you did not heat your system up properly, I believe jumping the > temperature from 0K up to 300 K could lead to bad van der Walls > interactions, which would cause your energy to drift. > > Hope that helps, > Ed > > On Mon, 3 Jan 2005, Peter Bazeley wrote: > > > Hello > > > > I am simulating a protein with NAMD, using a basic set of parameters. > > I minimize my protein for 1000 timesteps, then run for 50000 > > timesteps. I've found that the TOTAL energy of the system increases > > over time. I guess I'm trying to figure out the reason behind this. > > Could it be that I am seeing the entropic effects on the protein over > > time? Or perhaps the minimization created a structure that is lower in > > energy than would be expected in vivo, and the simulation brings the > > structure back to a more normal state? > > > > Thanks for any input, > > Peter Bazeley > > > From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 4 10:46:49 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j04GknRV006998 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 4 Jan 2005 10:46:49 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j04GknEu006997 for namd-l-outgoing; Tue, 4 Jan 2005 10:46:49 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from smtp-2.llnl.gov (smtp-2.llnl.gov [128.115.250.82]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j04GkmRU006993 for ; Tue, 4 Jan 2005 10:46:48 -0600 (CST) Received: from youkai.llnl.gov (localhost [127.0.0.1]) by smtp-2.llnl.gov (8.12.3p2-20030917/8.12.3/LLNL evision: 1.15 $) with ESMTP id j04GkfYJ029346; Tue, 4 Jan 2005 08:46:41 -0800 (PST) Received: from youkai.llnl.gov (youkai.llnl.gov [134.9.187.176]) by youkai.llnl.gov (8.12.11/8.12.10) with ESMTP id j04GkebF018610; Tue, 4 Jan 2005 08:46:40 -0800 Date: Tue, 4 Jan 2005 08:46:40 -0800 (PST) From: Brian Bennion To: bora erdemli cc: Ioana Cozmuta , namd-l@ks.uiuc.edu Subject: Re: namd-l: Bug alert!!! In-Reply-To: <20050104071337.17832.qmail@web40627.mail.yahoo.com> Message-ID: References: <20050104071337.17832.qmail@web40627.mail.yahoo.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Have you looked at the namdwiki page http://www.ks.uiuc.edu/Research/namd/wiki/?NamdTroubleshooting and excluded any of these possibilities? Brian On Mon, 3 Jan 2005, bora erdemli wrote: > Dear All; > > I need help about the following error occured during > simulation. > > Processor 0 Exiting: Called CmiAbort > > Reason: BUG ALERT: Stray PME grid charges > detected! > > BUG ALERT: NAMD has detected a bug. Please notify > namd@ks.uiuc.edu. > > req_handle_abort called > Fatal error on PE 0> BUG ALERT: Stray PME grid > charges > detected! > > BUG ALERT: NAMD has detected a bug. Please notify > namd@ks.uiuc.edu. > > I could visualize my system and everything seems to be > ok . I have some free charges around my system which I > did put them by using VMD autoionize plug-in in order > to neutralize the system. I made 10000 minimization by > using usual NAMD procedure no simulated annealing or > such modification. > > > --- Ioana Cozmuta wrote: > > > Did you vizualize your trajectory? Do you have free > > charges > > (counterions) around your system? What system are > > you looking at? What > > was your equilibration procedure? Do you see the > > system splitting > > > > If you give more information I might be able to help > > if none else has > > a better idea. > > > > Ioana > > > > > > -- > > Ioana Cozmuta, Ph.D. > > Eloret Corporation > > NASA Ames Research Center > > http://people.nas.nasa.gov/~ioana/ > > w (650) 604-0993, h (408) 732-1399 > > On Thu, 23 Dec 2004 23:06:32 -0800 (PST), bora > > erdemli > > wrote: > > > > > > Dear All; > > > > > > After almost 2 ns simulation , I faced with the > > > following error and my simulation was stopped. > > > What could be the reason? > > > > > > best regards.... > > > > > > ------------ Processor 0 Exiting: Called CmiAbort > > > ------------ > > > Reason: BUG ALERT: Stray PME grid charges > > detected! > > > > > > BUG ALERT: NAMD has detected a bug. Please notify > > > namd@ks.uiuc.edu. > > > > > > req_handle_abort called > > > Fatal error on PE 0> BUG ALERT: Stray PME grid > > charges > > > detected! > > > > > > BUG ALERT: NAMD has detected a bug. Please notify > > > namd@ks.uiuc.edu. > > > > > > ===== > > > Sabri Bora Erdemli > > > Koc University > > > Computational Science and Engineering > > > Research and Teaching Asistant > > > Koc Universitesi pk.218 34550 > > > sariyer Istanbul/TURKEY > > > tel no: 02123381736 > > > 05326512523 > > > > > > > > > __________________________________ > > > Do you Yahoo!? > > > Yahoo! Mail - You care about security. So do we. > > > http://promotions.yahoo.com/new_mail > > > > > > > > ===== > Sabri Bora Erdemli > Koc University > Computational Science and Engineering > Research and Teaching Asistant > Koc Universitesi pk.218 34550 > sariyer Istanbul/TURKEY > tel no: 02123381736 > 05326512523 > > > > > > > __________________________________ > Do you Yahoo!? > Send a seasonal email greeting and help others. Do good. > http://celebrity.mail.yahoo.com > ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1@llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 424-6605 ** ***************************************************************** From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 4 11:01:57 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j04H1uRV007579 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 4 Jan 2005 11:01:57 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j04H1uNc007578 for namd-l-outgoing; Tue, 4 Jan 2005 11:01:56 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from ipstpost.umd.edu (IDENT:root@ipstpost.umd.edu [129.2.9.228]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j04H1uRU007574 for ; Tue, 4 Jan 2005 11:01:56 -0600 (CST) Received: from lakers.umd.edu (sendmail@lakers.umd.edu [128.8.92.100]) by ipstpost.umd.edu (8.12.10/8.12.10) with ESMTP id j04H1sYL008885; Tue, 4 Jan 2005 12:01:54 -0500 (EST) Received: from localhost (edobrien@localhost) by lakers.umd.edu (8.12.10/8.12.10) with ESMTP id j04H1rZX017011; Tue, 4 Jan 2005 12:01:53 -0500 (EST) X-Authentication-Warning: lakers.umd.edu: edobrien owned process doing -bs Date: Tue, 4 Jan 2005 12:01:53 -0500 (EST) From: Edward Patrick Obrien X-X-Sender: edobrien@lakers.umd.edu To: Peter Bazeley cc: NAMD Subject: Re: namd-l: increase in energy over time In-Reply-To: <92be0d4505010319196b360505@mail.gmail.com> Message-ID: References: <92be0d4505010315275f90db99@mail.gmail.com> <92be0d4505010319196b360505@mail.gmail.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi Peter, If you are running periodic boundary conditions I don't think there should be a boundary energy. If you run non-periodic boundary conditions then I believe that these additional energy terms are added to the total energy. 300 K is roughly "room temperature", which I believe is the temperature many in vitro expermiments are carried out at. Your system will likely not change much in simulations between 300 and 310, unless your protein is cooperative to an extreme. So run at either temperature. Many of the questions you are asking are important to know, and understand. I suggest you read the documentation on the NAMD site, and do the online tutorials so you can get a good understanding of how to carry out MD sims. Also, there are also excellent books by Frenkel, and Leach that are a good introduction. Regards, Ed On Mon, 3 Jan 2005, Peter Bazeley wrote: > Hi Ed > > Thanks for your response. You are right in that there is a gradual > rise in both temperature and kinetic energy, which corresponds to the > rise in total energy. My total simulation time is only 100 ps, so I > imagine that jumping from a temperature of 0 to 300 would have a > significant effect. > > I know that in a simple force field equation, potential energy is the > sum of the bond, angle, improper, dihedral, electrostatic, and VDW > energies. Do you know if the boundary and miscellaneous energies get > added to that as well? > > It seems that 300K is a very common temperature in NAMD runs, yet > physiological conditions are closer to 310K. Do you know why 300 is > preferred? > > > Thanks again, > Peter Bazeley > > > On Mon, 3 Jan 2005 19:29:46 -0500 (EST), Edward Patrick Obrien > wrote: >> Hi Peter, >> In the microconanical ensemble (NVE) energy drift (change in total >> energy as a function of time) occurs due to finite integration errors >> associated with discretizing newton's equations of motion. >> Typically the total kinetic energy becomes more positive correlating with >> an increase in temperature. You should check these two quantities, and see >> if they are increasing. >> >> If you are running in the canonical (NVT) or Gibbs (NPT) ensemble your >> total energy should fluctuate. >> >> You want to avoid energy drift in NVE because it is non-physical, and >> can mess up your dynamics. >> >> To minimize energy drift make sure your system is well minimized >> (Gradient tolerance < 1.0 or less), heat your sytem in steps (I typically >> due it over the course of 300 ps) to the >> temperature desired, and use a reasonable time integration step >> (conventionally 1 fs at 300K). >> >> I don't believe you are seeing entropic effect, as the energy you are >> probably looking at is the energy of the system (which neglects the >> entropic term) and not the free energy. >> >> The minimization step is equivalent to carrying out a simulation at >> temperature equal to 0 K, because the motion is determine only by the >> gradient of the potential energy, and there is no kinetic term. Thus, if >> you did not heat your system up properly, I believe jumping the >> temperature from 0K up to 300 K could lead to bad van der Walls >> interactions, which would cause your energy to drift. >> >> Hope that helps, >> Ed >> >> On Mon, 3 Jan 2005, Peter Bazeley wrote: >> >>> Hello >>> >>> I am simulating a protein with NAMD, using a basic set of parameters. >>> I minimize my protein for 1000 timesteps, then run for 50000 >>> timesteps. I've found that the TOTAL energy of the system increases >>> over time. I guess I'm trying to figure out the reason behind this. >>> Could it be that I am seeing the entropic effects on the protein over >>> time? Or perhaps the minimization created a structure that is lower in >>> energy than would be expected in vivo, and the simulation brings the >>> structure back to a more normal state? >>> >>> Thanks for any input, >>> Peter Bazeley >>> >> > From owner-namd-l@halifax.ks.uiuc.edu Wed Jan 5 11:32:07 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j05HW7RV000637 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Wed, 5 Jan 2005 11:32:07 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j05HW7dM000636 for namd-l-outgoing; Wed, 5 Jan 2005 11:32:07 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from cancun.ks.uiuc.edu (cancun.ks.uiuc.edu [130.126.120.136]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j05HW6RU000631 for ; Wed, 5 Jan 2005 11:32:06 -0600 (CST) Received: (from jim@localhost) by cancun.ks.uiuc.edu (8.12.10+Sun/8.12.10/Submit) id j05HW6Yd008071 for namd-l@ks.uiuc.edu; Wed, 5 Jan 2005 11:32:06 -0600 (CST) Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.194]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j05CVCRU018398 for ; Wed, 5 Jan 2005 06:31:12 -0600 (CST) Received: by wproxy.gmail.com with SMTP id 70so595503wra for ; Wed, 05 Jan 2005 04:31:07 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding; b=CyWSFiAPgrlFAfPNWlvO2wxxWK9rifjlHXq6F/hE+eg71EzQwEiPgO/axz/si2qAjdO55F4XXYYxm3V9FRGbhzFOOANNWB+QZgkV+IY34mxpANqDGRYejG2an7I4ulMrDl8TZDllIdrtNvllGAO5aP2h1TrgCXuSOf74b+a7aCc= Received: by 10.54.52.62 with SMTP id z62mr346684wrz; Wed, 05 Jan 2005 04:31:07 -0800 (PST) Received: by 10.54.30.54 with HTTP; Wed, 5 Jan 2005 04:31:07 -0800 (PST) Message-ID: <92be0d4505010504312c4ead69@mail.gmail.com> Date: Wed, 5 Jan 2005 07:31:07 -0500 From: Peter Bazeley Reply-To: Peter Bazeley To: NAMD Subject: namd-l: tcoupling coefficient Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi all This is a simple question/answer, but I'd just like to be sure. In regards to the tCoupleFile/tCoupleCol parameters when using temperature coupling, is there any conversion/translation required for the coefficient values? In other words, if I want a coefficient of 0.1, can I simply put 0.1 in the PDB file? Thanks, Peter Bazeley From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 6 19:02:19 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0712JRV017759 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Thu, 6 Jan 2005 19:02:19 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0712JOQ017758 for namd-l-outgoing; Thu, 6 Jan 2005 19:02:19 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from hp.vpac.org (vpac.org [131.170.184.3]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0712HRU017751 for ; Thu, 6 Jan 2005 19:02:18 -0600 (CST) Received: from localhost (hp.vpac.org [127.0.0.1]) by hp.vpac.org (Postfix) with ESMTP id 0EA2BA1403C for ; Fri, 7 Jan 2005 12:02:08 +1100 (EST) Received: from hp.vpac.org ([127.0.0.1]) by localhost (hp.vpac.org [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 02842-03 for ; Fri, 7 Jan 2005 12:02:05 +1100 (EST) Received: from sys04.vpac.org (sys04.vpac.org [131.170.184.132]) by hp.vpac.org (Postfix) with ESMTP for ; Fri, 7 Jan 2005 12:02:05 +1100 (EST) Subject: namd-l: Compiling From: Damon Smith To: NAMD Content-Type: text/plain Date: Fri, 07 Jan 2005 12:02:04 +1100 Message-Id: <1105059724.25631.39.camel@sys04> Mime-Version: 1.0 X-Mailer: Evolution 2.0.2 Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new at vpac.org Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi all, I applied for a CVS key for namd but never got one. Are they difficult to get? I just wanted to check out the latest version, so I can compile it for the combination: mpi amd64 gcc myrinet. Which seems impossible to do properly without the newest version of namd. Damon From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 6 20:13:53 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j072DrRV019898 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Thu, 6 Jan 2005 20:13:53 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j072DrPd019897 for namd-l-outgoing; Thu, 6 Jan 2005 20:13:53 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from ipstpost.umd.edu (IDENT:root@ipstpost.umd.edu [129.2.9.228]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j072DqRU019893 for ; Thu, 6 Jan 2005 20:13:52 -0600 (CST) Received: from nolook.umd.edu (sendmail@nolook.umd.edu [128.8.92.47]) by ipstpost.umd.edu (8.12.10/8.12.10) with ESMTP id j072DpXK006833; Thu, 6 Jan 2005 21:13:51 -0500 (EST) Received: from localhost (dimar@localhost) by nolook.umd.edu (8.12.10/8.12.10) with ESMTP id j072Doe0019832; Thu, 6 Jan 2005 21:13:50 -0500 (EST) X-Authentication-Warning: nolook.umd.edu: dimar owned process doing -bs Date: Thu, 6 Jan 2005 21:13:50 -0500 (EST) From: Ruxandra Dima X-X-Sender: dimar@nolook.umd.edu To: Damon Smith cc: NAMD Subject: Re: namd-l: Compiling In-Reply-To: <1105059724.25631.39.camel@sys04> Message-ID: References: <1105059724.25631.39.camel@sys04> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk On Fri, 7 Jan 2005, Damon Smith wrote: > Hi all, > > I applied for a CVS key for namd but never got one. Are they difficult > to get? I just wanted to check out the latest version, so I can compile > it for the combination: mpi amd64 gcc myrinet. Which seems impossible > to do properly without the newest version of namd. > > Damon > > I never received one either. It's been about two weeks now and no info from them. I do not know why this is not working. Ruxandra From owner-namd-l@halifax.ks.uiuc.edu Fri Jan 7 04:50:00 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07Ao0RV005167 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 7 Jan 2005 04:50:00 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j07Ao0TH005166 for namd-l-outgoing; Fri, 7 Jan 2005 04:50:00 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from mangan.chem.au.dk (mangan.chem.au.dk [130.225.22.13]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with SMTP id j07AnxRU005155 for ; Fri, 7 Jan 2005 04:49:59 -0600 (CST) Received: (qmail 16739 invoked by uid 48); 7 Jan 2005 10:51:07 -0000 Received: from kem512-214-1.chem.au.dk (kem512-214-1.chem.au.dk [130.225.23.233]) by mail.chem.au.dk (IMP) with HTTP for ; Fri, 7 Jan 2005 11:51:07 +0100 Message-ID: <1105095067.41de699b6fc0e@mail.chem.au.dk> Date: Fri, 7 Jan 2005 11:51:07 +0100 From: lc@chem.au.dk To: namd-l@ks.uiuc.edu Subject: namd-l: parameters for NVT ensemble MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, I am trying to run a simulation in the NVT ensemble, but have a couple of practical questions regarding the choice of temperature control. What would an appropriate value be for the temperature coefficient when running a simulation in NVT ensemble with Berendsen temperature coupling? What about the Langevin coupling coefficient? So far we have only used Langevin dynamics in Stochatic Boundary simulations, so I am a bit confused about using it, as a means to controlling the temperature. I have seen previous posts on the list giving a value of 1 ps-1 is that a good value, or does it restrain the protein to much? Hope you can help me, thanks in advance Leyla Celik From owner-namd-l@halifax.ks.uiuc.edu Fri Jan 7 07:47:45 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07DljRV010184 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 7 Jan 2005 07:47:45 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j07DljU5010183 for namd-l-outgoing; Fri, 7 Jan 2005 07:47:45 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from poincare.ciril.fr (persmail.uhp-nancy.fr [194.214.217.19]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07DliRU010179 for ; Fri, 7 Jan 2005 07:47:44 -0600 (CST) Received: from dvorak.edam.uhp-nancy.fr (dvorak.edam.uhp-nancy.fr [194.57.168.80]) (authenticated bits=0) by poincare.ciril.fr (8.13.2/8.13.2/Guy-30-12-2004) with ESMTP id j07DlQ46007233 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Fri, 7 Jan 2005 14:47:27 +0100 (MET) From: =?iso-8859-1?q?J=E9r=F4me_H=E9nin?= To: lc@chem.au.dk Subject: Re: namd-l: parameters for NVT ensemble Date: Fri, 7 Jan 2005 14:58:12 +0100 User-Agent: KMail/1.7.1 Cc: namd-l@ks.uiuc.edu References: <1105095067.41de699b6fc0e@mail.chem.au.dk> In-Reply-To: <1105095067.41de699b6fc0e@mail.chem.au.dk> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Message-Id: <200501071458.12813.jerome.henin@uhp-nancy.fr> X-Spam-Score: 0 () X-Scanned-By: poincare.ciril.fr on 194.214.217.19 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id j07DljRU010180 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi Leyla, > What about the Langevin coupling coefficient? So far we have only used > Langevin dynamics in Stochatic Boundary simulations, so I am a bit confused > about using it, as a means to controlling the temperature. I have seen > previous posts on the list giving a value of 1 ps-1 is that a good value, > or does it restrain the protein to much? I would say: use the smallest value that keeps your temperature reasonably constant, to stay close to Newtonian dynamics (at least on short timescales). If nothing terrible is happening in your system, 0.1 or 0.2 ps-1 might be enough. Jerome -- J閞鬽e H閚in Equipe de Dynamique des Assemblages Membranaires Universit Henri Poincar / CNRS UMR 7565 B.P. 239 54506 Vandoeuvre-l鑣-Nancy Cedex Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71 http://www.edam.uhp-nancy.fr/ From owner-namd-l@halifax.ks.uiuc.edu Fri Jan 7 11:51:57 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07HpvRV022555 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 7 Jan 2005 11:51:57 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j07HpvV4022554 for namd-l-outgoing; Fri, 7 Jan 2005 11:51:57 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from smtpvip2.bnl.gov (smtp@smtpgateway.BNL.GOV [130.199.3.132]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07HpuRU022550 for ; Fri, 7 Jan 2005 11:51:56 -0600 (CST) Received: from exchange10.b459.bnl.gov ([130.199.74.42] helo=exchange10.bnl.gov) by smtpvip2.bnl.gov with esmtp (bnl.gov SMTP) id 1CmyHD-00088x-00 for ; Fri, 07 Jan 2005 12:51:55 -0500 Received: by exchange10.b459.bnl.gov with Internet Mail Service (5.5.2657.72) id ; Fri, 7 Jan 2005 12:51:55 -0500 Message-ID: <47B8E77FE2707145932EADD8C529D77F01CD02FF@exchange10.b459.bnl.gov> From: "Stern, Julie" To: "'namd-l@ks.uiuc.edu'" Subject: namd-l: namd on lemieux Date: Fri, 7 Jan 2005 12:51:53 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain X-BNL-MailScanner-Information: Please contact the ITD Service Desk for more information X-BNL-MailScanner: Found to be clean X-BNL-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=0.009, required 5, autolearn=disabled, AWL 0.01) X-MailScanner-From: jvstern@bnl.gov Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hello, Has anyone successfully run NAMD on lemieux? I'm having a prmtop reading error (for a prmtop file which is read successfully on my local machines) and don't know if its a NAMD 2.4 vs 2.5 problem or that it can't find the file and is a scripting or prun problem. Can you share a sample script file with the prun call and do we have to generate the node list first? Thanks. --jule From owner-namd-l@halifax.ks.uiuc.edu Fri Jan 7 17:29:30 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07NTURV008098 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 7 Jan 2005 17:29:30 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j07NTTns008097 for namd-l-outgoing; Fri, 7 Jan 2005 17:29:29 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from cancun.ks.uiuc.edu (cancun.ks.uiuc.edu [130.126.120.136]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07NTTRU008093 for ; Fri, 7 Jan 2005 17:29:29 -0600 (CST) Received: (from jim@localhost) by cancun.ks.uiuc.edu (8.12.10+Sun/8.12.10/Submit) id j07NTTXB010148 for namd-l@ks.uiuc.edu; Fri, 7 Jan 2005 17:29:29 -0600 (CST) Received: from mail.charite.de (mail.charite.de [160.45.207.131]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07N1FRV007009 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 7 Jan 2005 17:01:16 -0600 (CST) Received: from localhost (localhost [127.0.0.1]) by mail.charite.de (Postfix) with ESMTP id 88387220964 for ; Sat, 8 Jan 2005 00:01:16 +0100 (CET) Received: from mail.charite.de ([127.0.0.1]) by localhost (mail.charite.de [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id 14134-06 for ; Sat, 8 Jan 2005 00:01:15 +0100 (CET) Received: from postamt.charite.de (postamt.charite.de [10.47.2.164]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (Client did not present a certificate) by mail.charite.de (Postfix) with ESMTP id 0F110220963 for ; Sat, 8 Jan 2005 00:01:14 +0100 (CET) Received: from [141.42.58.117] (ronja.bioch.charite.de [141.42.58.117]) by postamt.charite.de (Postfix) with ESMTP id 3F37A220E99 for ; Sat, 8 Jan 2005 00:01:12 +0100 (CET) Message-ID: <41DF14B9.7060503@charite.de> Date: Sat, 08 Jan 2005 00:01:13 +0100 From: Jan Saam User-Agent: Mozilla Thunderbird 0.8 (X11/20041221) X-Accept-Language: en-us, en MIME-Version: 1.0 To: namd-l@ks.uiuc.edu Subject: namd-l: tclForces - addforce to group of atoms X-Enigmail-Version: 0.86.0.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: amavisd-new at charite.de Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi all, does anyone know what exactly happens when I apply a force to a group of atoms using the tcl intrface? Assume something like this: I speccify a group of 5 atoms using "addgroup" ten I apply a force of 1000 kcal/mol/A to it. Will each atom be pulled with 1000 kcal/mol/A or will the force be distributed among the atoms so that each one feels only 200 kcal/mol/A. Or is the force even scaled with the mass? Example: tclForcesScript { set group [addgroup 1 2 3 7 10] proc calcforces {} { global group ... # do stuff addforce $group 1000 } Thanks for help, Jan From owner-namd-l@halifax.ks.uiuc.edu Fri Jan 7 17:33:56 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07NXuRV008254 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 7 Jan 2005 17:33:56 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j07NXuGZ008253 for namd-l-outgoing; Fri, 7 Jan 2005 17:33:56 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from cancun.ks.uiuc.edu (cancun.ks.uiuc.edu [130.126.120.136]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07NXtRU008249 for ; Fri, 7 Jan 2005 17:33:55 -0600 (CST) Received: (from jim@localhost) by cancun.ks.uiuc.edu (8.12.10+Sun/8.12.10/Submit) id j07NXtiG010180 for namd-l@ks.uiuc.edu; Fri, 7 Jan 2005 17:33:55 -0600 (CST) Received: from mail.charite.de (mail.charite.de [160.45.207.131]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j07NReRV008027 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 7 Jan 2005 17:27:41 -0600 (CST) Received: from localhost (localhost [127.0.0.1]) by mail.charite.de (Postfix) with ESMTP id 47B4C22095F for ; Sat, 8 Jan 2005 00:27:42 +0100 (CET) Received: from mail.charite.de ([127.0.0.1]) by localhost (mail.charite.de [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id 24796-01 for ; Sat, 8 Jan 2005 00:27:40 +0100 (CET) Received: from postamt.charite.de (postamt.charite.de [10.47.2.164]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (Client did not present a certificate) by mail.charite.de (Postfix) with ESMTP id C2528220964 for ; Sat, 8 Jan 2005 00:27:40 +0100 (CET) Received: from [141.42.58.117] (ronja.bioch.charite.de [141.42.58.117]) by postamt.charite.de (Postfix) with ESMTP id BB5492206D2 for ; Sat, 8 Jan 2005 00:27:38 +0100 (CET) Message-ID: <41DF1AEC.9070208@charite.de> Date: Sat, 08 Jan 2005 00:27:40 +0100 From: Jan Saam User-Agent: Mozilla Thunderbird 0.8 (X11/20041221) X-Accept-Language: en-us, en MIME-Version: 1.0 To: namd-l@ks.uiuc.edu Subject: namd-l: tclForces - addforce to group of atoms X-Enigmail-Version: 0.86.0.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: amavisd-new at charite.de Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk In my previous email there was an error: the force should be appied with: addforce $group {1000 0 0} rather than addforce $group 1000 Sorry, Jan From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 14:32:49 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j08KWnRV006706 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 14:32:49 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j08KWnxk006705 for namd-l-outgoing; Sat, 8 Jan 2005 14:32:49 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from smtpvip2.bnl.gov (smtp@smtpgateway.BNL.GOV [130.199.3.132]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j08KWmRU006701 for ; Sat, 8 Jan 2005 14:32:48 -0600 (CST) Received: from exchange10.b459.bnl.gov ([130.199.74.42] helo=exchange10.bnl.gov) by smtpvip2.bnl.gov with esmtp (bnl.gov SMTP) id 1CnNGQ-0001zg-00 for ; Sat, 08 Jan 2005 15:32:46 -0500 Received: by exchange10.b459.bnl.gov with Internet Mail Service (5.5.2657.72) id ; Sat, 8 Jan 2005 15:32:47 -0500 Message-ID: <47B8E77FE2707145932EADD8C529D77F01CD0304@exchange10.b459.bnl.gov> From: "Stern, Julie" To: "'namd-l@ks.uiuc.edu'" Subject: namd-l: restarting a simulation accurately Date: Sat, 8 Jan 2005 15:32:41 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain X-BNL-MailScanner-Information: Please contact the ITD Service Desk for more information X-BNL-MailScanner: Found to be clean X-BNL-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=0.008, required 5, autolearn=disabled, AWL 0.01) X-MailScanner-From: jvstern@bnl.gov Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hello, Does anyone know how to continue a job from the restart files where the velocity information will be read as well as the coordinate information? Also, if just the coordinate information is read (with 'coordinates filename', how would you explain that type of restart, all atoms start from the same place but are kicked in a different direction - and is this even a repeatable simlation? Would it obtain the velocity info anyway by default from the beta column of the coordinate file or does it have to be read in from the .vel file? Thanks. --Julie From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 15:03:52 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j08L3qRV007260 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 15:03:52 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j08L3pd3007257 for namd-l-outgoing; Sat, 8 Jan 2005 15:03:51 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.196]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j08L3pRU007247 for ; Sat, 8 Jan 2005 15:03:51 -0600 (CST) Received: by rproxy.gmail.com with SMTP id 1so713957rny for ; Sat, 08 Jan 2005 13:03:50 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding; b=Au9ZrnbUUCk9p4VqwcQhlF7du73TNTmlxorGI9+Lnl3oRsCSCdyQNlsX8n2rUCr8Sbl1H1UcN1shvwnQcX1TPfwJw3P9g+w4xsa6pYcgLm/1Amx4UIC6SRJDNaylWwh6S0Dr4tqfXwUkvAGpt3gjViqw0gJZPODSu3BFkRBIYVA= Received: by 10.38.206.12 with SMTP id d12mr754857rng; Sat, 08 Jan 2005 13:03:50 -0800 (PST) Received: by 10.38.8.35 with HTTP; Sat, 8 Jan 2005 13:03:50 -0800 (PST) Message-ID: <8adccabf050108130347a343ee@mail.gmail.com> Date: Sat, 8 Jan 2005 16:03:50 -0500 From: Charles Danko Reply-To: Charles Danko To: namd-l@ks.uiuc.edu Subject: namd-l: Harmonic restraints for moving residue positions?? Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, I am trying to move the N and C terminus tails to positions that they are likely to take such that I can dock models of two domains. Since I can calculate approximately where this point is going to be, I was thinking of using harmonic restraints to move the tails of both proteins into their approximate position. Does anyone see any problems with this approach? Should the values listed in a previous thread of consexp =2 and the force constant = 5 be adequate to work in this situation?? If I decide to go with a higher force constant, do you advise that I ramp up to this higher number? And finally, should I apply force to only one atom (e.g. the backbone N, or backbone C for moving N and C respectively), or do you recommend applying forces to the entire residue? Many thanks for all answers/ suggestions. Charles From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 15:06:26 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j08L6QRV007353 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 15:06:26 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j08L6QSe007352 for namd-l-outgoing; Sat, 8 Jan 2005 15:06:26 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.204]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j08L6PRU007347 for ; Sat, 8 Jan 2005 15:06:25 -0600 (CST) Received: by rproxy.gmail.com with SMTP id 1so714011rny for ; Sat, 08 Jan 2005 13:06:25 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:references; b=bXi2l3s5lTUvyhFOdY0qMITr3KzxOwNWPPoq9w6IKn79dlkUbcSw24TnxuQoHVNWj1J8gelNfUwFsExe7u5Di2Ql2m21Lx1V3JvfGiSU2D+DHdy2Pb0ADc19QPYHaAks3wCblHR00/FIarTs0gaikjWXxjZN7XP7k36vXb3kMxE= Received: by 10.38.8.13 with SMTP id 13mr749559rnh; Sat, 08 Jan 2005 13:06:24 -0800 (PST) Received: by 10.38.8.35 with HTTP; Sat, 8 Jan 2005 13:06:24 -0800 (PST) Message-ID: <8adccabf0501081306640abc0@mail.gmail.com> Date: Sat, 8 Jan 2005 16:06:24 -0500 From: Charles Danko Reply-To: Charles Danko To: "Stern, Julie" Subject: Re: namd-l: restarting a simulation accurately Cc: "namd-l@ks.uiuc.edu" In-Reply-To: <47B8E77FE2707145932EADD8C529D77F01CD0304@exchange10.b459.bnl.gov> Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit References: <47B8E77FE2707145932EADD8C529D77F01CD0304@exchange10.b459.bnl.gov> Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Using the velocity or binvelocity command you can specify the velocity file. You can search previous threads on thsi forum for more information. Also, you can specify where the last simulation started using the "firsttimestep" parameter. Look in the namd users guide for more details on this. Good luck! Charles On Sat, 8 Jan 2005 15:32:41 -0500, Stern, Julie wrote: > Hello, > Does anyone know how to continue a job from the > restart files where the velocity information will be > read as well as the coordinate information? > Also, if just the coordinate information is read (with > 'coordinates filename', how would you explain that type of restart, all > atoms start from the same place but are kicked in a different direction - > and is this even a repeatable simlation? Would it obtain the velocity > info anyway by default from the beta column of the coordinate file or > does it have to be read in from the .vel file? > > Thanks. > > --Julie > From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 20:39:59 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j092dwRV014358 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 20:39:58 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j092dwEB014357 for namd-l-outgoing; Sat, 8 Jan 2005 20:39:58 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from outgoing-mail.its.caltech.edu (outgoing-mail.its.caltech.edu [131.215.49.69]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j092dwRU014353 for ; Sat, 8 Jan 2005 20:39:58 -0600 (CST) Received: from earth-dog (earth-dog [192.168.1.3]) by water-ox-postvirus (Postfix) with ESMTP id BB41926ACB0 for ; Sat, 8 Jan 2005 18:39:52 -0800 (PST) Received: from earth-ox ([192.168.1.9]) by earth-dog (MailMonitor for SMTP v1.2.2 ) ; Sat, 8 Jan 2005 18:39:52 -0800 (PST) Received: from [192.168.1.102] (adsl-66-120-58-8.dsl.lsan03.pacbell.net [66.120.58.8]) by earth-ox.its.caltech.edu (Postfix) with ESMTP id DB2F0109A0C for ; Sat, 8 Jan 2005 18:39:50 -0800 (PST) User-Agent: Microsoft-Entourage/11.1.0.040913 Date: Sat, 08 Jan 2005 18:39:45 -0800 Subject: namd-l: Error in when using charmrun From: Eric Peterson To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Status: No, hits=0.0 tagged_above=-100000.0 required=5.0 X-Spam-Level: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk I'm trying to get a parallel run going on a Linux Alpha cluster here at Caltech... Things seem to start okay but then I run into a cryptic error about something called "CWeb performance data"?? Has anyone run into this error before? Here's the output to standard error: ----- Charmrun> charmrun started... Charmrun> using /tmp/74750.alicante.aero.caltech.edu.nodelist as nodesfile Charmrun> rsh (n02:0d) started Charmrun> rsh (n01:1d) started Charmrun> node programs all started Charmrun> node programs all connected ------------- Processor 1 Exiting: Called CmiAbort ------------ Reason: CWeb performance data sent to wrong processor... req_handle_abort called Fatal error on PE 1> CWeb performance data sent to wrong processor... ----- And the output from standard out: ----- Charmrun rsh(n01.1)> remote responding... Charmrun rsh(n01.1)> starting node-program... Charmrun rsh(n01.1)> rsh phase successful. Charmrun rsh(n02.0)> remote responding... Charmrun rsh(n02.0)> starting node-program... Charmrun rsh(n02.0)> rsh phase successful. Charmrun> adding client 0: "n02", IP:10.1.0.102 Charmrun> adding client 1: "n01", IP:10.1.0.101 Charmrun> Charmrun = 10.1.0.102, port = 4544 Charmrun> Sending "0 10.1.0.102 4544 14893 0" to client 0. Charmrun> Starting rsh n02 -l peterson /bin/sh -f Charmrun> Sending "1 10.1.0.102 4544 14893 0" to client 1. Charmrun> Starting rsh n01 -l peterson /bin/sh -f Charmrun> waiting for rsh (n02:0), pid 14894 Charmrun> waiting for rsh (n01:1), pid 14895 Charmrun> Waiting for 0-th client to connect. Charmrun> client 0 connected (IP=10.1.0.102 data_port=1242) Charmrun> Waiting for 1-th client to connect. Charmrun> client 1 connected (IP=10.1.0.101 data_port=1030) Charmrun> All clients connected. Charmrun> IP tables sent. -- Eric From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 21:00:18 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0930IRV014851 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 21:00:18 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0930ILw014850 for namd-l-outgoing; Sat, 8 Jan 2005 21:00:18 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from sccimhc92.asp.att.net (sccimhc92.asp.att.net [63.240.76.166]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0930HRU014841 for ; Sat, 8 Jan 2005 21:00:18 -0600 (CST) Received: from [192.168.2.5] (12-221-82-55.client.insightbb.com[12.221.82.55]) by sccimhc92.asp.att.net (sccimhc92) with ESMTP id <20050109030004i9200ithtue>; Sun, 9 Jan 2005 03:00:04 +0000 Message-ID: <41E09E33.7030601@ks.uiuc.edu> Date: Sat, 08 Jan 2005 21:00:03 -0600 From: Gengbin Zheng User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Eric Peterson CC: namd-l@ks.uiuc.edu Subject: Re: namd-l: Error in when using charmrun References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Something pretty bad happened here, probably not in charmrun. The message seemed to be corrupted and delivered to a wrong function. We haven't tested on Linux Alpha for a long time. I can't tell for sure why this happens. could you try run this again, but with "+netpoll" option, which disables asynchronous I/O interruption. Gengbin Eric Peterson wrote: >I'm trying to get a parallel run going on a Linux Alpha cluster here at >Caltech... Things seem to start okay but then I run into a cryptic error >about something called "CWeb performance data"?? Has anyone run into this >error before? > >Here's the output to standard error: > >----- > >Charmrun> charmrun started... >Charmrun> using /tmp/74750.alicante.aero.caltech.edu.nodelist as nodesfile >Charmrun> rsh (n02:0d) started >Charmrun> rsh (n01:1d) started >Charmrun> node programs all started >Charmrun> node programs all connected >------------- Processor 1 Exiting: Called CmiAbort ------------ >Reason: CWeb performance data sent to wrong processor... > >req_handle_abort called >Fatal error on PE 1> CWeb performance data sent to wrong processor... > >----- > >And the output from standard out: > >----- > >Charmrun rsh(n01.1)> remote responding... >Charmrun rsh(n01.1)> starting node-program... >Charmrun rsh(n01.1)> rsh phase successful. >Charmrun rsh(n02.0)> remote responding... >Charmrun rsh(n02.0)> starting node-program... >Charmrun rsh(n02.0)> rsh phase successful. >Charmrun> adding client 0: "n02", IP:10.1.0.102 >Charmrun> adding client 1: "n01", IP:10.1.0.101 >Charmrun> Charmrun = 10.1.0.102, port = 4544 >Charmrun> Sending "0 10.1.0.102 4544 14893 0" to client 0. >Charmrun> Starting rsh n02 -l peterson /bin/sh -f >Charmrun> Sending "1 10.1.0.102 4544 14893 0" to client 1. >Charmrun> Starting rsh n01 -l peterson /bin/sh -f >Charmrun> waiting for rsh (n02:0), pid 14894 >Charmrun> waiting for rsh (n01:1), pid 14895 >Charmrun> Waiting for 0-th client to connect. >Charmrun> client 0 connected (IP=10.1.0.102 data_port=1242) >Charmrun> Waiting for 1-th client to connect. >Charmrun> client 1 connected (IP=10.1.0.101 data_port=1030) >Charmrun> All clients connected. >Charmrun> IP tables sent. > > >-- Eric > > > > From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 21:16:56 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j093GuRV015274 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 21:16:56 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j093Gupn015273 for namd-l-outgoing; Sat, 8 Jan 2005 21:16:56 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from outgoing-mail.its.caltech.edu (outgoing-mail.its.caltech.edu [131.215.49.69]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j093GsRU015258; Sat, 8 Jan 2005 21:16:54 -0600 (CST) Received: from earth-dog (earth-dog [192.168.1.3]) by earth-ox-postvirus (Postfix) with ESMTP id 11556109ABF; Sat, 8 Jan 2005 19:16:49 -0800 (PST) Received: from water-ox ([192.168.1.10]) by earth-dog (MailMonitor for SMTP v1.2.2 ) ; Sat, 8 Jan 2005 19:16:48 -0800 (PST) Received: from [192.168.1.102] (adsl-66-120-58-8.dsl.lsan03.pacbell.net [66.120.58.8]) by water-ox.its.caltech.edu (Postfix) with ESMTP id C6E6B26AC04; Sat, 8 Jan 2005 19:16:47 -0800 (PST) User-Agent: Microsoft-Entourage/11.1.0.040913 Date: Sat, 08 Jan 2005 19:16:47 -0800 Subject: Re: namd-l: Error in when using charmrun From: Eric Peterson To: Gengbin Zheng Cc: NAMD Message-ID: In-Reply-To: <41E09E33.7030601@ks.uiuc.edu> Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Status: No, hits=0.0 tagged_above=-100000.0 required=5.0 X-Spam-Level: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk I tried running charmrun with the "+netpoll" and "++netpoll" options and it doesn't recognize either one.... Maybe the Linux Alpha build of charm++ is outdated and doesn't include that option?? Eric On 1/8/05 7:00 PM, "Gengbin Zheng" wrote: > > Something pretty bad happened here, probably not in charmrun. The > message seemed to be corrupted and delivered to a wrong function. > We haven't tested on Linux Alpha for a long time. I can't tell for sure > why this happens. > could you try run this again, but with "+netpoll" option, which disables > asynchronous I/O interruption. > > Gengbin > > Eric Peterson wrote: > >> I'm trying to get a parallel run going on a Linux Alpha cluster here at >> Caltech... Things seem to start okay but then I run into a cryptic error >> about something called "CWeb performance data"?? Has anyone run into this >> error before? >> >> Here's the output to standard error: >> >> ----- >> >> Charmrun> charmrun started... >> Charmrun> using /tmp/74750.alicante.aero.caltech.edu.nodelist as nodesfile >> Charmrun> rsh (n02:0d) started >> Charmrun> rsh (n01:1d) started >> Charmrun> node programs all started >> Charmrun> node programs all connected >> ------------- Processor 1 Exiting: Called CmiAbort ------------ >> Reason: CWeb performance data sent to wrong processor... >> >> req_handle_abort called >> Fatal error on PE 1> CWeb performance data sent to wrong processor... >> >> ----- >> >> And the output from standard out: >> >> ----- >> >> Charmrun rsh(n01.1)> remote responding... >> Charmrun rsh(n01.1)> starting node-program... >> Charmrun rsh(n01.1)> rsh phase successful. >> Charmrun rsh(n02.0)> remote responding... >> Charmrun rsh(n02.0)> starting node-program... >> Charmrun rsh(n02.0)> rsh phase successful. >> Charmrun> adding client 0: "n02", IP:10.1.0.102 >> Charmrun> adding client 1: "n01", IP:10.1.0.101 >> Charmrun> Charmrun = 10.1.0.102, port = 4544 >> Charmrun> Sending "0 10.1.0.102 4544 14893 0" to client 0. >> Charmrun> Starting rsh n02 -l peterson /bin/sh -f >> Charmrun> Sending "1 10.1.0.102 4544 14893 0" to client 1. >> Charmrun> Starting rsh n01 -l peterson /bin/sh -f >> Charmrun> waiting for rsh (n02:0), pid 14894 >> Charmrun> waiting for rsh (n01:1), pid 14895 >> Charmrun> Waiting for 0-th client to connect. >> Charmrun> client 0 connected (IP=10.1.0.102 data_port=1242) >> Charmrun> Waiting for 1-th client to connect. >> Charmrun> client 1 connected (IP=10.1.0.101 data_port=1030) >> Charmrun> All clients connected. >> Charmrun> IP tables sent. >> >> >> -- Eric >> >> >> >> > From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 21:20:16 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j093KGRV015363 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 21:20:16 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j093KGfE015362 for namd-l-outgoing; Sat, 8 Jan 2005 21:20:16 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from sccimhc92.asp.att.net (sccimhc92.asp.att.net [63.240.76.166]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j093KFRU015356 for ; Sat, 8 Jan 2005 21:20:15 -0600 (CST) Received: from [192.168.2.5] (12-221-82-55.client.insightbb.com[12.221.82.55]) by sccimhc92.asp.att.net (sccimhc92) with ESMTP id <20050109032009i9200isdhce>; Sun, 9 Jan 2005 03:20:10 +0000 Message-ID: <41E0A2E8.8040207@ks.uiuc.edu> Date: Sat, 08 Jan 2005 21:20:08 -0600 From: Gengbin Zheng User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Eric Peterson CC: NAMD Subject: Re: namd-l: Error in when using charmrun References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Which version of charm/namd is this? It must be very old. You can try charm >= 5.8, NAMD 2.5 source. Gengbin Eric Peterson wrote: >I tried running charmrun with the "+netpoll" and "++netpoll" options and it >doesn't recognize either one.... Maybe the Linux Alpha build of charm++ is >outdated and doesn't include that option?? > >Eric > > >On 1/8/05 7:00 PM, "Gengbin Zheng" wrote: > > > >>Something pretty bad happened here, probably not in charmrun. The >>message seemed to be corrupted and delivered to a wrong function. >>We haven't tested on Linux Alpha for a long time. I can't tell for sure >>why this happens. >>could you try run this again, but with "+netpoll" option, which disables >>asynchronous I/O interruption. >> >>Gengbin >> >>Eric Peterson wrote: >> >> >> >>>I'm trying to get a parallel run going on a Linux Alpha cluster here at >>>Caltech... Things seem to start okay but then I run into a cryptic error >>>about something called "CWeb performance data"?? Has anyone run into this >>>error before? >>> >>>Here's the output to standard error: >>> >>>----- >>> >>>Charmrun> charmrun started... >>>Charmrun> using /tmp/74750.alicante.aero.caltech.edu.nodelist as nodesfile >>>Charmrun> rsh (n02:0d) started >>>Charmrun> rsh (n01:1d) started >>>Charmrun> node programs all started >>>Charmrun> node programs all connected >>>------------- Processor 1 Exiting: Called CmiAbort ------------ >>>Reason: CWeb performance data sent to wrong processor... >>> >>>req_handle_abort called >>>Fatal error on PE 1> CWeb performance data sent to wrong processor... >>> >>>----- >>> >>>And the output from standard out: >>> >>>----- >>> >>>Charmrun rsh(n01.1)> remote responding... >>>Charmrun rsh(n01.1)> starting node-program... >>>Charmrun rsh(n01.1)> rsh phase successful. >>>Charmrun rsh(n02.0)> remote responding... >>>Charmrun rsh(n02.0)> starting node-program... >>>Charmrun rsh(n02.0)> rsh phase successful. >>>Charmrun> adding client 0: "n02", IP:10.1.0.102 >>>Charmrun> adding client 1: "n01", IP:10.1.0.101 >>>Charmrun> Charmrun = 10.1.0.102, port = 4544 >>>Charmrun> Sending "0 10.1.0.102 4544 14893 0" to client 0. >>>Charmrun> Starting rsh n02 -l peterson /bin/sh -f >>>Charmrun> Sending "1 10.1.0.102 4544 14893 0" to client 1. >>>Charmrun> Starting rsh n01 -l peterson /bin/sh -f >>>Charmrun> waiting for rsh (n02:0), pid 14894 >>>Charmrun> waiting for rsh (n01:1), pid 14895 >>>Charmrun> Waiting for 0-th client to connect. >>>Charmrun> client 0 connected (IP=10.1.0.102 data_port=1242) >>>Charmrun> Waiting for 1-th client to connect. >>>Charmrun> client 1 connected (IP=10.1.0.101 data_port=1030) >>>Charmrun> All clients connected. >>>Charmrun> IP tables sent. >>> >>> >>>-- Eric >>> >>> >>> >>> >>> >>> > > > > From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 22:24:31 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j094OVRV016874 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 22:24:31 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j094OV1T016873 for namd-l-outgoing; Sat, 8 Jan 2005 22:24:31 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from outgoing-mail.its.caltech.edu (outgoing-mail.its.caltech.edu [131.215.49.69]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j094ORRU016863; Sat, 8 Jan 2005 22:24:28 -0600 (CST) Received: from water-dog (water-dog [192.168.1.26]) by water-ox-postvirus (Postfix) with ESMTP id 1A26626AC62; Sat, 8 Jan 2005 20:24:18 -0800 (PST) Received: from earth-ox ([192.168.1.9]) by water-dog (MailMonitor for SMTP v1.2.2 ) ; Sat, 8 Jan 2005 20:24:17 -0800 (PST) Received: from [192.168.1.102] (adsl-66-120-58-8.dsl.lsan03.pacbell.net [66.120.58.8]) by earth-ox.its.caltech.edu (Postfix) with ESMTP id 8A629109A47; Sat, 8 Jan 2005 20:24:15 -0800 (PST) User-Agent: Microsoft-Entourage/11.1.0.040913 Date: Sat, 08 Jan 2005 20:24:11 -0800 Subject: Re: namd-l: Error in when using charmrun From: Eric Peterson To: Gengbin Zheng Cc: NAMD Message-ID: In-Reply-To: <41E0A2E8.8040207@ks.uiuc.edu> Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Status: No, hits=0.0 tagged_above=-100000.0 required=5.0 X-Spam-Level: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk The thing is, the version of NAMD I downloaded is the NAMD 2.5 build for Linux Alpha... Here's the info from namd2 --h: Info: NAMD 2.5 for Linux-Alpha Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd@ks.uiuc.edu Info: Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 050612 for net-linux-axp-cxx Info: Built Fri Sep 26 17:27:35 CDT 2003 by jim on proteus.ks.uiuc.edu Isn't this version the latest build? Eric On 1/8/05 7:20 PM, "Gengbin Zheng" wrote: > > Which version of charm/namd is this? It must be very old. > You can try charm >= 5.8, NAMD 2.5 source. > > Gengbin > > > Eric Peterson wrote: > >> I tried running charmrun with the "+netpoll" and "++netpoll" options and it >> doesn't recognize either one.... Maybe the Linux Alpha build of charm++ is >> outdated and doesn't include that option?? >> >> Eric >> >> >> On 1/8/05 7:00 PM, "Gengbin Zheng" wrote: >> >> >> >>> Something pretty bad happened here, probably not in charmrun. The >>> message seemed to be corrupted and delivered to a wrong function. >>> We haven't tested on Linux Alpha for a long time. I can't tell for sure >>> why this happens. >>> could you try run this again, but with "+netpoll" option, which disables >>> asynchronous I/O interruption. >>> >>> Gengbin >>> >>> Eric Peterson wrote: >>> >>> >>> >>>> I'm trying to get a parallel run going on a Linux Alpha cluster here at >>>> Caltech... Things seem to start okay but then I run into a cryptic error >>>> about something called "CWeb performance data"?? Has anyone run into this >>>> error before? >>>> >>>> Here's the output to standard error: >>>> >>>> ----- >>>> >>>> Charmrun> charmrun started... >>>> Charmrun> using /tmp/74750.alicante.aero.caltech.edu.nodelist as nodesfile >>>> Charmrun> rsh (n02:0d) started >>>> Charmrun> rsh (n01:1d) started >>>> Charmrun> node programs all started >>>> Charmrun> node programs all connected >>>> ------------- Processor 1 Exiting: Called CmiAbort ------------ >>>> Reason: CWeb performance data sent to wrong processor... >>>> >>>> req_handle_abort called >>>> Fatal error on PE 1> CWeb performance data sent to wrong processor... >>>> >>>> ----- >>>> >>>> And the output from standard out: >>>> >>>> ----- >>>> >>>> Charmrun rsh(n01.1)> remote responding... >>>> Charmrun rsh(n01.1)> starting node-program... >>>> Charmrun rsh(n01.1)> rsh phase successful. >>>> Charmrun rsh(n02.0)> remote responding... >>>> Charmrun rsh(n02.0)> starting node-program... >>>> Charmrun rsh(n02.0)> rsh phase successful. >>>> Charmrun> adding client 0: "n02", IP:10.1.0.102 >>>> Charmrun> adding client 1: "n01", IP:10.1.0.101 >>>> Charmrun> Charmrun = 10.1.0.102, port = 4544 >>>> Charmrun> Sending "0 10.1.0.102 4544 14893 0" to client 0. >>>> Charmrun> Starting rsh n02 -l peterson /bin/sh -f >>>> Charmrun> Sending "1 10.1.0.102 4544 14893 0" to client 1. >>>> Charmrun> Starting rsh n01 -l peterson /bin/sh -f >>>> Charmrun> waiting for rsh (n02:0), pid 14894 >>>> Charmrun> waiting for rsh (n01:1), pid 14895 >>>> Charmrun> Waiting for 0-th client to connect. >>>> Charmrun> client 0 connected (IP=10.1.0.102 data_port=1242) >>>> Charmrun> Waiting for 1-th client to connect. >>>> Charmrun> client 1 connected (IP=10.1.0.101 data_port=1030) >>>> Charmrun> All clients connected. >>>> Charmrun> IP tables sent. >>>> >>>> >>>> -- Eric >>>> >>>> >>>> >>>> >>>> >>>> >> >> >> >> > From owner-namd-l@halifax.ks.uiuc.edu Sat Jan 8 22:50:32 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j094oWRV017418 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sat, 8 Jan 2005 22:50:32 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j094oWgC017417 for namd-l-outgoing; Sat, 8 Jan 2005 22:50:32 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from sccimhc91.asp.att.net (sccimhc91.asp.att.net [63.240.76.165]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j094oVRU017412 for ; Sat, 8 Jan 2005 22:50:31 -0600 (CST) Received: from [192.168.2.5] (12-221-82-55.client.insightbb.com[12.221.82.55]) by sccimhc91.asp.att.net (sccimhc91) with ESMTP id <20050109045026i9100bpsu8e>; Sun, 9 Jan 2005 04:50:26 +0000 Message-ID: <41E0B810.8000901@ks.uiuc.edu> Date: Sat, 08 Jan 2005 22:50:24 -0600 From: Gengbin Zheng User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Eric Peterson CC: NAMD Subject: Re: namd-l: Error in when using charmrun References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk The binary was indeed tested on the machine we had, however it was more than one year old, and I don't know if there is any upgrade on the system libraries which may cause some compatibility problem. You may have to compile from source. I think we no long have that machine, otherwise I can run some test. Gengbin Eric Peterson wrote: >The thing is, the version of NAMD I downloaded is the NAMD 2.5 build for >Linux Alpha... Here's the info from namd2 --h: > >Info: NAMD 2.5 for Linux-Alpha >Info: >Info: Please visit http://www.ks.uiuc.edu/Research/namd/ >Info: and send feedback or bug reports to namd@ks.uiuc.edu >Info: >Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999) >Info: in all publications reporting results obtained with NAMD. >Info: >Info: Based on Charm++/Converse 050612 for net-linux-axp-cxx >Info: Built Fri Sep 26 17:27:35 CDT 2003 by jim on proteus.ks.uiuc.edu > >Isn't this version the latest build? > >Eric > > > > >On 1/8/05 7:20 PM, "Gengbin Zheng" wrote: > > > >>Which version of charm/namd is this? It must be very old. >>You can try charm >= 5.8, NAMD 2.5 source. >> >>Gengbin >> >> >>Eric Peterson wrote: >> >> >> >>>I tried running charmrun with the "+netpoll" and "++netpoll" options and it >>>doesn't recognize either one.... Maybe the Linux Alpha build of charm++ is >>>outdated and doesn't include that option?? >>> >>>Eric >>> >>> >>>On 1/8/05 7:00 PM, "Gengbin Zheng" wrote: >>> >>> >>> >>> >>> >>>>Something pretty bad happened here, probably not in charmrun. The >>>>message seemed to be corrupted and delivered to a wrong function. >>>>We haven't tested on Linux Alpha for a long time. I can't tell for sure >>>>why this happens. >>>>could you try run this again, but with "+netpoll" option, which disables >>>>asynchronous I/O interruption. >>>> >>>>Gengbin >>>> >>>>Eric Peterson wrote: >>>> >>>> >>>> >>>> >>>> >>>>>I'm trying to get a parallel run going on a Linux Alpha cluster here at >>>>>Caltech... Things seem to start okay but then I run into a cryptic error >>>>>about something called "CWeb performance data"?? Has anyone run into this >>>>>error before? >>>>> >>>>>Here's the output to standard error: >>>>> >>>>>----- >>>>> >>>>>Charmrun> charmrun started... >>>>>Charmrun> using /tmp/74750.alicante.aero.caltech.edu.nodelist as nodesfile >>>>>Charmrun> rsh (n02:0d) started >>>>>Charmrun> rsh (n01:1d) started >>>>>Charmrun> node programs all started >>>>>Charmrun> node programs all connected >>>>>------------- Processor 1 Exiting: Called CmiAbort ------------ >>>>>Reason: CWeb performance data sent to wrong processor... >>>>> >>>>>req_handle_abort called >>>>>Fatal error on PE 1> CWeb performance data sent to wrong processor... >>>>> >>>>>----- >>>>> >>>>>And the output from standard out: >>>>> >>>>>----- >>>>> >>>>>Charmrun rsh(n01.1)> remote responding... >>>>>Charmrun rsh(n01.1)> starting node-program... >>>>>Charmrun rsh(n01.1)> rsh phase successful. >>>>>Charmrun rsh(n02.0)> remote responding... >>>>>Charmrun rsh(n02.0)> starting node-program... >>>>>Charmrun rsh(n02.0)> rsh phase successful. >>>>>Charmrun> adding client 0: "n02", IP:10.1.0.102 >>>>>Charmrun> adding client 1: "n01", IP:10.1.0.101 >>>>>Charmrun> Charmrun = 10.1.0.102, port = 4544 >>>>>Charmrun> Sending "0 10.1.0.102 4544 14893 0" to client 0. >>>>>Charmrun> Starting rsh n02 -l peterson /bin/sh -f >>>>>Charmrun> Sending "1 10.1.0.102 4544 14893 0" to client 1. >>>>>Charmrun> Starting rsh n01 -l peterson /bin/sh -f >>>>>Charmrun> waiting for rsh (n02:0), pid 14894 >>>>>Charmrun> waiting for rsh (n01:1), pid 14895 >>>>>Charmrun> Waiting for 0-th client to connect. >>>>>Charmrun> client 0 connected (IP=10.1.0.102 data_port=1242) >>>>>Charmrun> Waiting for 1-th client to connect. >>>>>Charmrun> client 1 connected (IP=10.1.0.101 data_port=1030) >>>>>Charmrun> All clients connected. >>>>>Charmrun> IP tables sent. >>>>> >>>>> >>>>>-- Eric >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >>> >>> > > > > From owner-namd-l@halifax.ks.uiuc.edu Sun Jan 9 11:00:52 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j09H0qRV005246 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sun, 9 Jan 2005 11:00:52 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j09H0qJu005245 for namd-l-outgoing; Sun, 9 Jan 2005 11:00:52 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from sccimhc92.asp.att.net (sccimhc92.asp.att.net [63.240.76.166]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j09H0oRU005239 for ; Sun, 9 Jan 2005 11:00:51 -0600 (CST) Received: from [192.168.2.5] (12-221-82-55.client.insightbb.com[12.221.82.55]) by sccimhc92.asp.att.net (sccimhc92) with ESMTP id <20050109170045i9200isk6qe>; Sun, 9 Jan 2005 17:00:45 +0000 Message-ID: <41E1633B.2040207@ks.uiuc.edu> Date: Sun, 09 Jan 2005 11:00:43 -0600 From: Gengbin Zheng User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Damon Smith CC: NAMD Subject: Re: namd-l: Compiling References: <1105059724.25631.39.camel@sys04> In-Reply-To: <1105059724.25631.39.camel@sys04> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk I don't know what's going on. Unfortunately, I don't have the permission to modify the passwd file. For those of you who needs the source urgently, please download it from: http://www.ks.uiuc.edu/~gzheng/namd2.tar.gz. It includes Ruxandra's fixes for gcc 3.4. Please be hurry, it won't be there for too long. Sorry about the inconvenience. Gengbin Damon Smith wrote: >Hi all, > >I applied for a CVS key for namd but never got one. Are they difficult >to get? I just wanted to check out the latest version, so I can compile >it for the combination: mpi amd64 gcc myrinet. Which seems impossible >to do properly without the newest version of namd. > >Damon > > From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 10 11:13:08 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0AHD8RV010631 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 10 Jan 2005 11:13:08 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0AHD80J010630 for namd-l-outgoing; Mon, 10 Jan 2005 11:13:08 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from vscani-e.ucl.ac.uk (vscani-e.ucl.ac.uk [144.82.108.33]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0AHD6RV010625 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 10 Jan 2005 11:13:07 -0600 (CST) Received: from chemc253.chem.ucl.ac.uk ([128.40.156.253] helo=volta.chem.ucl.ac.uk) by vscani-e.ucl.ac.uk with esmtp (Exim 4.34) id 1Co35u-0004PD-RL for namd-l@ks.uiuc.edu; Mon, 10 Jan 2005 17:12:43 +0000 Received: from volta.chem.ucl.ac.uk (localhost [127.0.0.1]) by volta.chem.ucl.ac.uk (8.12.11/8.12.10) with ESMTP id j0AHCgpl022131 for ; Mon, 10 Jan 2005 17:12:42 GMT Received: from localhost (localhost [[UNIX: localhost]]) by volta.chem.ucl.ac.uk (8.12.11/8.12.11/Submit) id j0AHCgvC022130 for namd-l@ks.uiuc.edu; Mon, 10 Jan 2005 17:12:42 GMT From: Philip Fowler To: NAMD Subject: namd-l: thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials Date: Mon, 10 Jan 2005 17:12:41 +0000 User-Agent: KMail/1.6.2 MIME-Version: 1.0 Content-Disposition: inline Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Message-Id: <200501101712.41879.p.w.fowler@qmul.ac.uk> X-UCL-MailScanner-Information: Please contact the UCL Helpdesk, helpdesk@ucl.ac.uk for more information X-UCL-MailScanner: Found to be clean X-UCL-MailScanner-SpamCheck: X-MailScanner-From: philip@chemc253.chem.ucl.ac.uk Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi everyone, I have already run one calculation of a difference in binding free energy using the FEP module within NAMD. I am about to start calculating a second and need your help . In my first calculation (and this will happen again) I encountered the well-known "end-point catastrophe" where, because the van der Waals component is scaled linearly by lambda, the repulsive term remains and prevents the water exploring the void created when the atom has truly vanished. One solution to this is to follow the "separation-shifted" method of Zacharias, Straatsma & McCammon (J Chem Phys 100 9025 (1994)) where, for nonbonded interactions with alchemicalk atoms, the conventional vdW LJ form V = (1-lambda) [ A/r^12 - B/r^6 ] is replaced by V = (1-lambda) [ A/(r^2 +dlambda)^6 - B/(r^2 +dlambda)^3 ] (where dlambda is a supplied parameter) which is the same when lambda = 1. This form allows a much smoother transition as lambda=0,1 is approached. Now the questions are, 1) how and where would one change this in the source code? I have had a rummage but understanding the object structure would take me more time than I would like (I am not an expert at C++). In principal the logic is simple: for alchemical nonbonded vdw interactions, apply the new functional form, for everything else, keep it as it is. 2) would this be useful to anyone else? Thanks, --Phil -- Philip Fowler, PhD Student Centre for Computational Science, UCL Chemistry From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 10 15:58:32 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0ALwWRV022260 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 10 Jan 2005 15:58:32 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0ALwWe8022259 for namd-l-outgoing; Mon, 10 Jan 2005 15:58:32 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from poincare.ciril.fr (poincare.uhp-nancy.fr [194.214.217.19]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0ALwURU022255 for ; Mon, 10 Jan 2005 15:58:30 -0600 (CST) Received: from [192.168.1.253] (vandoeuvre-1-82-66-255-188.fbx.proxad.net [82.66.255.188]) (authenticated bits=0) by poincare.ciril.fr (8.13.2/8.13.2/Guy-30-12-2004) with ESMTP id j0ALwJ3j025359; Mon, 10 Jan 2005 22:58:21 +0100 (MET) From: =?iso-8859-1?q?J=E9r=F4me_H=E9nin?= To: Philip Fowler Subject: Re: namd-l: thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials Date: Mon, 10 Jan 2005 22:57:01 +0100 User-Agent: KMail/1.7.2 Cc: NAMD References: <200501101712.41879.p.w.fowler@qmul.ac.uk> In-Reply-To: <200501101712.41879.p.w.fowler@qmul.ac.uk> MIME-Version: 1.0 Content-Disposition: inline Content-Type: text/plain; charset="iso-8859-1" Message-Id: <200501102257.01327.jerome.henin@uhp-nancy.fr> X-Spam-Score: 0 () X-Scanned-By: poincare.ciril.fr on 194.214.217.19 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id j0ALwVRU022256 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi Philip, You are pointing out an issue I am concerned about too, and possibly the main weakness of the current alchemical FEP module. I mentioned it briefly to people in the Schulten group when I last visited them, but since it was not my main purpose, we did not come to any useful conclusion on that. As you say, implementing a separation-shifted potential does not raise any conceptual problem. A programmer familiar with NAMD and in particular the force-field implmentation should only need a reasonable amount of work to get it done. The problem boils down to the following: the group of people in the community that actually master most of the NAMD code is, as far as I know, small. Possibly very small. When alchemical FEP was contributed by our group, the post-doc who coded it had to spend a long time just to get familiar with the NAMD code. Now we would very much like to add such improvements as soft-core potentials, but we do not currently have the manpower for it. If you can contribute to an implementation, it will definitely be a significant advance for all users of this method. The best way I can imagine for now is to involve Klaus Schulten, who has access to both manpower and, obviously, technical knowledge concerning NAMD. Anyway, we commonly use that code, and there are ways to try to circumvent the end-point problem. The main point is a careful design of the windows, employing a large number of smaller and smaller windows as lambda approaches 1. I can send you an example config file tomorrow. Another improvement I have thought of recently is to replace the FEP formula with an overlap sampling method, for instance Bennett's method (see Lu, Singh and Kofke, J Chem Phys 118 (2003)). This significantly improves convergence for FEP calculations with a limited sampling. This is doable with the current version of the code, by post-processing the energy data output by the FEP module. I have a small program that does it. Anyone interested can just email me. Unfortunately, it is of no help with regard to the end-point catastrophe, because overlap sampling is often not feasible in the very last window. I will not expand on the reasons here - they are probably obvious to specialists and not so interesting to non-specialists. Thanks for raising that point! Best, Jerome Le Lundi 10 Janvier 2005 18:12, Philip Fowler a 閏rit: > Hi everyone, > > I have already run one calculation of a difference in binding free energy > using the FEP module within NAMD. I am about to start calculating a second > and need your help . > > In my first calculation (and this will happen again) I encountered the > well-known "end-point catastrophe" where, because the van der Waals > component is scaled linearly by lambda, the repulsive term remains and > prevents the water exploring the void created when the atom has truly > vanished. > > One solution to this is to follow the "separation-shifted" method of > Zacharias, Straatsma & McCammon (J Chem Phys 100 9025 (1994)) where, for > nonbonded interactions with alchemicalk atoms, the conventional vdW LJ form > > V = (1-lambda) [ A/r^12 - B/r^6 ] > > is replaced by > > V = (1-lambda) [ A/(r^2 +dlambda)^6 - B/(r^2 +dlambda)^3 ] > > (where dlambda is a supplied parameter) > > which is the same when lambda = 1. This form allows a much smoother > transition as lambda=0,1 is approached. > > Now the questions are, > > 1) how and where would one change this in the source code? I have had a > rummage but understanding the object structure would take me more time than > I would like (I am not an expert at C++). In principal the logic is simple: > for alchemical nonbonded vdw interactions, apply the new functional form, > for everything else, keep it as it is. > > 2) would this be useful to anyone else? > > Thanks, > > --Phil -- J閞鬽e H閚in Equipe de Dynamique des Assemblages Membranaires Universit Henri Poincar / CNRS UMR 7565 B.P. 239 54506 Vandoeuvre-l鑣-Nancy Cedex Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71 http://www.edam.uhp-nancy.fr/ From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 11 01:53:16 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0B7rGRV010883 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 11 Jan 2005 01:53:16 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0B7rGc9010882 for namd-l-outgoing; Tue, 11 Jan 2005 01:53:16 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from mangan.chem.au.dk (mangan.chem.au.dk [130.225.22.13]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with SMTP id j0B7rERU010874 for ; Tue, 11 Jan 2005 01:53:15 -0600 (CST) Received: (qmail 9569 invoked by uid 48); 11 Jan 2005 07:54:54 -0000 Received: from kem512-214-1.chem.au.dk (kem512-214-1.chem.au.dk [130.225.23.233]) by mail.chem.au.dk (IMP) with HTTP for ; Tue, 11 Jan 2005 08:54:54 +0100 Message-ID: <1105430094.41e3864e91ed5@mail.chem.au.dk> Date: Tue, 11 Jan 2005 08:54:54 +0100 From: lc@chem.au.dk To: namd-l@ks.uiuc.edu Subject: namd-l: namdstats MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, I am trying to run the script 'namdstats' downloaded from the NAMD homepage. When using it on a minimization log-file I get the following warning, no matter which frames I give as input. Does anyone know what to do? I am not familiar with tcl scripts... N 0 awk: cmd. line:1: fatal: division by zero attempted Thanks Leyla From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 11 05:52:57 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0BBqvRV016869 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 11 Jan 2005 05:52:57 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0BBqvdU016868 for namd-l-outgoing; Tue, 11 Jan 2005 05:52:57 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from nobel.phys.uni.torun.pl (nobel.phys.uni.torun.pl [158.75.5.90]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0BBquRU016858 for ; Tue, 11 Jan 2005 05:52:56 -0600 (CST) Received: by nobel.phys.uni.torun.pl (Postfix, from userid 5134) id 4836113F5D9; Tue, 11 Jan 2005 12:52:48 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by nobel.phys.uni.torun.pl (Postfix) with ESMTP id 397D213F5CE for ; Tue, 11 Jan 2005 12:52:48 +0100 (CET) Date: Tue, 11 Jan 2005 12:52:48 +0100 (CET) From: Slawomir Orlowski To: namd-l@ks.uiuc.edu Subject: namd-l: AMD64 or PIV Prescott ... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-MailScanner-Information: Please contact the ISP for more information X-MailScanner: Found to be clean X-MailScanner-SpamCheck: not spam, SpamAssassin (score=0, required 5) X-MailScanner-From: bigman@phys.uni.torun.pl Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, I am going to buy a few computers (4-5) for NAMD computations. What is the best choose: AMD Athlon64 3000+ or Intel PIV Prescott 2.4GHz FSB533? Thanks, Slawek Orlowski e-mail: bigman@phys.uni.torun.pl home page: http://www.phys.uni.torun.pl/~bigman Theoretical Biophysics Group Intitute of Physic Nicolas Copernicus University in Torun, Poland From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 11 08:43:10 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0BEhARV021230 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 11 Jan 2005 08:43:10 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0BEhAYm021229 for namd-l-outgoing; Tue, 11 Jan 2005 08:43:10 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from smtp206.mail.sc5.yahoo.com (smtp206.mail.sc5.yahoo.com [216.136.129.96]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with SMTP id j0BEh9RU021223 for ; Tue, 11 Jan 2005 08:43:09 -0600 (CST) Received: from unknown (HELO ?192.168.0.141?) (kitty?wxq@202.114.78.142 with plain) by smtp206.mail.sc5.yahoo.com with SMTP; 11 Jan 2005 14:43:07 -0000 Subject: namd-l: equilibrated the system From: Xiaoqing Wang To: NAMD Content-Type: text/plain; charset=utf-8 Message-Id: <1105454597.6779.10.camel@molecule> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.6 (1.4.6-2) Date: Tue, 11 Jan 2005 22:43:17 +0800 Content-Transfer-Encoding: 8bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi all I have downloaded an example of an equilibration (or 鈥渞estrained鈥) run input file(restrained_md_example.in) in web site http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm . #forcefield paratypecharmm on parameters par_all27_prot_lipid.inp #molecules structure ions_added.psf coordinates ions_added.pdb bincoordinates after_min.restart.coor #binvelocities a.restart.vel extendedSystem after_min.xsc temperature 310 #reassignFreq 100 #reassignTemp 25 #reassignIncr 25 #reassignHold 300 #constraints constraints on consref protein_only.coor conskfile protein_cons.pdb conskcol X #temp & pressure coupling langevin on langevinTemp 10 langevinDamping 1 #useGroupPressure yes #useFlexibleCell no #LangevinPiston on #LangevinPistonTarget 1 #LangevinPistonPeriod 200 #LangevinPistonDecay 500 #LangevinPistonTemp 10 #output outputname restr_md outputEnergies 10 restartfreq 500 DCDfreq 500 binaryoutput no binaryrestart yes outputTiming 100 wrapAll on wrapNearest on #integrator timestep 1 nonbondedFreq 1 fullElectFrequency 4 stepspercycle 20 #approximations rigidBonds all rigidTolerance 0.00000001 cutoff 12 switching on switchdist 10 pairlistdist 14 margin 3 exclude scaled1-4 1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber PME on #cellBasisVector1 114.39 0 0 #cellBasisVector2 0 120.16 0 #cellBasisVector3 0 0 141.96 PMEGridSizeX 120 PMEGridSizeY 120 PMEGridSizeZ 120 #minimize 1000 run 250000 My question is how to prepare consref and conskfile files if I want to restrain protein? Thanks!!! -- Wuhan University Wuhan China From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 11 09:59:06 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0BFx6RV023841 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 11 Jan 2005 09:59:06 -0600 (CST) Received: (from majordom@localhost) by halifax.ks.uiuc.edu (8.12.10/8.12.9/Submit) id j0BFx68Z023840 for namd-l-outgoing; Tue, 11 Jan 2005 09:59:06 -0600 (CST) X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from mta3.sucs.soton.ac.uk (mta3.sucs.soton.ac.uk [152.78.128.142]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j0BFx4RV023836 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Tue, 11 Jan 2005 09:59:05 -0600 (CST) Received: from thruxton.iss.soton.ac.uk (thruxton.iss.soton.ac.uk [152.78.129.91]) by mta3.sucs.soton.ac.uk (8.12.10/8.12.10) with ESMTP id j0BFwR7G016938 for ; Tue, 11 Jan 2005 15:58:28 GMT Received: (from nobody@localhost) by thruxton.iss.soton.ac.uk (8.12.10/8.12.10) id j0BFwRVX021161 for namd-l@ks.uiuc.edu; Tue, 11 Jan 2005 15:58:27 GMT X-Authentication-Warning: thruxton.iss.soton.ac.uk: nobody set sender to apw397@soton.ac.uk using -f Received: from 164.143.244.34 ([164.143.244.34]) by webmail.s