From owner-namd-l@rama.ks.uiuc.edu Fri Jan 2 12:06:46 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i02I6ktX009892 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 2 Jan 2004 12:06:46 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i02I6kLt009891 for namd-l-outgoing; Fri, 2 Jan 2004 12:06:46 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from nyssa.bchs.uh.edu (Nyssa.BCHS.UH.EDU [129.7.238.204]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i02I6gtX009879 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT); Fri, 2 Jan 2004 12:06:43 -0600 (CST) Received: from nyssa.bchs.uh.edu (localhost.localdomain [127.0.0.1]) by nyssa.bchs.uh.edu (8.12.10/8.12.9) with ESMTP id i02I4fG6030628; Fri, 2 Jan 2004 12:04:41 -0600 Received: from localhost (localhost [[UNIX: localhost]]) by nyssa.bchs.uh.edu (8.12.10/8.12.10/Submit) id i02I4fkD030627; Fri, 2 Jan 2004 12:04:41 -0600 From: Jerry Ebalunode Reply-To: jebalunode@UH.EDU Organization: University of Houston To: Gengbin Zheng Subject: Re: namd-l: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 Date: Fri, 2 Jan 2004 12:04:41 -0600 User-Agent: KMail/1.5.4 References: In-Reply-To: Cc: namd-l@ks.uiuc.edu MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200401021204.41329.jebalunode@uh.edu> Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi Gengbin, Sorry it took so long to get back to you. Well here is output during the compilation charm++ using intel c+ compiler version 8 [jebalunode@mckinley charm]$ ./build charm++ mpi-linux-ia64 ecc Selected Compiler: ecc Selected Options: Copying src/scripts/Makefile to mpi-linux-ia64-ecc/tmp Soft-linking over bin Soft-linking over lib Soft-linking over lib_so Soft-linking over include Soft-linking over tmp Generating mpi-linux-ia64-ecc/tmp/conv-mach-pre.sh Performing 'make charm++ OPTS=' in mpi-linux-ia64-ecc/tmp make headerlinks make[1]: Entering directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' ../bin/charmc -native -language c++ -cp ../bin/ -o charmxi xi-main.o xi-symbol.o xi-grammar.tab.o xi-scan.o xi-util.o sdag-globals.o CSdagConstruct.o CEntry.o ../bin/charmc -intrinsic -build-shared ckcallback.ci ../bin/charmc -intrinsic -build-shared ckmarshall.ci ../bin/charmc -intrinsic -build-shared ckarray.ci ../bin/charmc -intrinsic -build-shared cklocation.ci ../bin/charmc -intrinsic -build-shared ckreduction.ci ../bin/charmc -intrinsic -build-shared ckarrayreductionmgr.ci ../bin/charmc -intrinsic -build-shared tempo.ci ../bin/charmc -intrinsic -build-shared waitqd.ci ../bin/charmc -intrinsic -build-shared ckfutures.ci ../bin/charmc -intrinsic -build-shared ckcheckpoint.ci ../bin/charmc -intrinsic -build-shared LBDatabase.ci ../bin/charmc -intrinsic -build-shared CentralLB.ci ../bin/charmc -intrinsic -build-shared ComboCentLB.ci ../bin/charmc -intrinsic -build-shared NullLB.ci ../bin/charmc -intrinsic -build-shared RandCentLB.ci ../bin/charmc -intrinsic -build-shared RecBisectBfLB.ci ../bin/charmc -intrinsic -build-shared BaseLB.ci ../bin/charmc -intrinsic -build-shared MetisLB.ci ../bin/charmc -intrinsic -build-shared DummyLB.ci ../bin/charmc -intrinsic -build-shared RefineLB.ci ../bin/charmc -intrinsic -build-shared RefineCommLB.ci ../bin/charmc -intrinsic -build-shared OrbLB.ci ../bin/charmc -intrinsic -build-shared GreedyLB.ci ../bin/charmc -intrinsic -build-shared NborBaseLB.ci ../bin/charmc -intrinsic -build-shared NeighborLB.ci ../bin/charmc -intrinsic -build-shared NeighborCommLB.ci ../bin/charmc -intrinsic -build-shared WSLB.ci ../bin/charmc -intrinsic -build-shared GreedyRefLB.ci ../bin/charmc -intrinsic -build-shared RandRefLB.ci ../bin/charmc -intrinsic -build-shared GreedyCommLB.ci ../bin/charmc -intrinsic -build-shared Comm1LB.ci ../bin/charmc -intrinsic -build-shared EveryLB.ci ../bin/charmc -intrinsic -build-shared charisma.ci ../bin/charmc -intrinsic -build-shared trace-summary.ci ../bin/charmc -intrinsic -build-shared BlueGene.ci Soft-linking headers... make[1]: [headerlinks] Error 1 (ignored) touch headerlinks make[1]: Leaving directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' touch basics make charm-target make[1]: Entering directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' make headerlinks make[2]: Entering directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' make[2]: `headerlinks' is up to date. make[2]: Leaving directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' touch basics make QuickThreads/libqt.a make[2]: Entering directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' make[2]: `QuickThreads/libqt.a' is up to date. make[2]: Leaving directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' make converse-target make[2]: Entering directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' ../bin/charmc -build-shared -c -I. convcore.c convcore.c(2004): warning #266: function declared implicitly CmiTimerInit(); ^ ../bin/charmc -build-shared -c -I. conv-conds.c ../bin/charmc -build-shared -c -I. queueing.c ../bin/charmc -build-shared -c -I. msgmgr.c ../bin/charmc -build-shared -c -I. cpm.c ../bin/charmc -build-shared -c -I. cpthreads.c ../bin/charmc -build-shared -c -I. futures.c ../bin/charmc -build-shared -c -I. cldb.c ../bin/charmc -build-shared -c -I. topology.C ../bin/charmc -build-shared -c -I. random.c ../bin/charmc -build-shared -c -I. debug-conv.c ../bin/charmc -build-shared -c -I. generate.c ../bin/charmc -build-shared -c -I. edgelist.c edgelist.c(58): warning #1193: standard requires that parameter "x" be given a type by a subsequent declaration ("int" assumed) int edgeExists(x,y) ^ edgelist.c(58): warning #1193: standard requires that parameter "y" be given a type by a subsequent declaration ("int" assumed) int edgeExists(x,y) ^ ../bin/charmc -build-shared -c -I. conv-ccs.c ccs-server.c(311): warning #266: function declared implicitly if (isxdigit(key[0]) && isxdigit(key[1])) ^ ccs-server.c(353): warning #167: argument of type "unsigned int *far" is incompatible with parameter of type "int *far" ccs_server_fd=skt_server(&port); ^ ccs-server.c(416): warning #167: argument of type "unsigned int *far" is incompatible with parameter of type "int *far" fd=skt_accept(ccs_server_fd,&ip,&port); ^ ../bin/charmc -build-shared -c -I. ccs-builtins.C ../bin/charmc -build-shared -c -I. traceCore.C traceCoreAPI.h(8): warning #380: linkage specification is incompatible with previous "Cpv__traceCoreOn_" (declared at line 20 of "traceCore.h") CpvExtern(int,_traceCoreOn); ^ ../bin/charmc -build-shared -c -I. traceCoreCommon.C traceCoreAPI.h(8): warning #380: linkage specification is incompatible with previous "Cpv__traceCoreOn_" (declared at line 20 of "traceCore.h") CpvExtern(int,_traceCoreOn); ^ ../bin/charmc -build-shared -c -I. converseProjections.C ../bin/charmc -build-shared -c -I. machineProjections.C ../bin/charmc -build-shared -c -I. quiescence.c ../bin/charmc -build-shared -c -I. isomalloc.c ../bin/charmc -build-shared -c -I. global-nop.c ../bin/charmc -build-shared -o ../lib/libconv-core.a convcore.o conv-conds.o queueing.o msgmgr.o cpm.o cpthreads.o futures.o cldb.o topology.o random.o debug-conv.o generate.o edgelist.o conv-ccs.o ccs-builtins.o traceCore.o traceCoreCommon.o converseProjections.o machineProjections.o quiescence.o isomalloc.o global-nop.o Warning: creating ../lib_so/libconv-core.so /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_inactive /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_inactive /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_current_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_current_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_current_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_current_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_current_ /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol Csv_CtvOffsCpthread_errcode_ Fatal Error by charmc in directory /tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp Command icc -L/opt/scali/lib -lmpi -o ../lib_so/libconv-core.so -shared -L/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/lib_so convcore.o conv-conds.o queueing.o msgmgr.o cpm.o cpthreads.o futures.o cldb.o topology.o random.o debug-conv.o generate.o edgelist.o conv-ccs.o ccs-builtins.o traceCore.o traceCoreCommon.o converseProjections.o machineProjections.o quiescence.o isomalloc.o global-nop.o returned error code 1 charmc exiting... make[2]: *** [../lib/libconv-core.a] Error 1 make[2]: Leaving directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' make[1]: *** [converse] Error 2 make[1]: Leaving directory `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' make: *** [charm++] Error 2 On Wednesday 31 December 2003 01:25 pm, Gengbin Zheng wrote: > I don't have access to Intel C++ compilers v8.0 on IA64. Could you copy me > the compile error messages? > > Gengbin > > On Wed, 31 Dec 2003, Jerry Ebalunode wrote: > > Hi, > > I would like to know if Charm++ and then NAMD can be built using the new > > intel C++ compiler version 8.0 on an IA64 arch. I already tried this on > > the charm++ source code that was provided along with the namd ver2.5., > > with no succes in compling charm++ for mpi-linux-ia64. > > > > On Wednesday 31 December 2003 11:59 am, Gengbin Zheng wrote: > > > Oops, forgot to mention, you need to recompile Linux version of NAMD > > > from scratch also. The pre-compiled version is not compatiable with the > > > latest CVS version due to my recent changes in structure layout. Also, > > > the pre-compiled version is built with Intel C++ compiler which I have > > > not tested the compatibility with Win32 VC++ yet. So I would suggest > > > going with gcc on Linux before I tested it with Intel C++. > > > > > > Since I don't know which verison of Linux you are running, I don't know > > > how to make pre-compiled binary for you. But compiling for Linux is > > > fairely easy, check out: > > > http://www.ks.uiuc.edu/Research/namd/development.html > > > Please download both Charm++ and NAMD source from the two different CVS > > > servers. > > > > > > I myself rarely use tcl and plugins features (being a mostly Charm++ > > > developer). Based on my limited knowledge, tcl is used to enable > > > scripting features (so you can write tcl scripts in config file), and > > > plugins tools are from VMD's Plugins to enable trajectory analysis. The > > > NAMD user manual should have more detailed information. > > > > > > Gengbin > > > > > > On Wed, 31 Dec 2003, Gadi Oron wrote: > > > > On Wed, 2003-12-31 at 02:05, Gengbin Zheng wrote: > > > > > Hi, > > > > > > > > > > Please find the NAMD binary compiled with Windows VC++ 6.0 at: > > > > > http://www.ks.uiuc.edu/~gzheng/NAMD_Win32-i686.zip > > > > > > > > Thank you, but still no luck... > > > > I manage to start NAMD alone on a Win2K node and on Linux node, > > > > so probably my nodelist is Ok. But together I get either: > > > > > > > > Info: SUMMARY OF PARAMETERS: > > > > Info: 180 BONDS > > > > Info: 442 ANGLES > > > > Info: 534 DIHEDRAL > > > > Info: 50 IMPROPER > > > > Info: 91 VDW > > > > Info: 0 VDW_PAIRS > > > > Charmrun: error on request socket-- > > > > Error on socket recv! > > > > > > > > when the Linux box is first in the nodelist and: > > > > > > > > Charmrun> node programs all connected > > > > ------------- Processor 1 Exiting: Caught Signal ------------ > > > > Signal: segmentation violation > > > > Suggestion: Try running with '++debug', or linking with '-memory > > > > paranoid'. > > > > Fatal error on PE 1> segmentation violation > > > > > > > > when the order is inverted. > > > > > > > > I am using charmd compiled from the last source and NAMD 2.5 from > > > > the pre-compiled binaries for linux and your Windows executables. > > > > > > > > Any idea? > > > > > > > > Best regards. > > > > > > > > P.S. It is not really explained what "plugins" and "tcl" libraries > > > > are needed for... Could you give me a hint on that? > > > > -- > > > > ================= Gadi ORON, PhD -o- Proteologics > > > > ====================== ========== gadi/at/proteologics.com ========== > > > > +972 8 9475666 ========== The questions remain the same. The answers > > > > are eternally variable. > > > > -- > > Cheers, > > > > Jerry Ebalunode > > Graduate Research Assistant > > RM 402F Houston Science Center > > Phone: 713-743-8367 > > Dept. of Biology and Biochemistry > > University of Houston. > > 4800 Calhoun Road > > Houston, TX 77204 -- Cheers, Jerry Ebalunode Graduate Research Assistant RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston. 4800 Calhoun Road Houston, TX 77204 From owner-namd-l@rama.ks.uiuc.edu Fri Jan 2 12:09:56 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i02I9ttX010002 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 2 Jan 2004 12:09:55 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i02I9tvY010001 for namd-l-outgoing; Fri, 2 Jan 2004 12:09:55 -0600 (CST) X-Authentication-Warning: rama.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 [130.126.120.65]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i02I9ptY009997 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT); Fri, 2 Jan 2004 12:09:51 -0600 (CST) Date: Fri, 2 Jan 2004 12:09:51 -0600 (CST) From: Gengbin Zheng To: Gadi Oron cc: namd-l@ks.uiuc.edu, Subject: Re: namd-l: Charm++ nodelist commands In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk > > > Another question: is it possible to set process priority (nice level) > > > for NAMD node programs? > > > > > > > No. It can be implemented but not for windows I guess. > > You can now. This has been implemented in Charm++ CVS server. It is only for non windows versions. Nice level can be passed in command line using +nice n, for example: ./charmrun +p2 ./pgm +nice 10 will set process priority for all node processes to 10. This currently works for all net-* and mpi-* verisons of Charm++. For net-* versions when nodelist file is readed, one can set process specific nice value in nodelist too, for example: group main host host1 +nice 10 host host2 +nice 8 Note that the nice value normally ranges from -20 to 20, but may be system dependent. Setting negative value needs root privilege, the program will abort when error occurs. Please let me know if you have any problem when using this new feature. Gengbin From owner-namd-l@rama.ks.uiuc.edu Fri Jan 2 12:16:33 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i02IGXtX010234 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 2 Jan 2004 12:16:33 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i02IGXnZ010233 for namd-l-outgoing; Fri, 2 Jan 2004 12:16:33 -0600 (CST) X-Authentication-Warning: rama.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 [130.126.120.65]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i02IGWtY010229 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT); Fri, 2 Jan 2004 12:16:32 -0600 (CST) Date: Fri, 2 Jan 2004 12:16:32 -0600 (CST) From: Gengbin Zheng To: Jerry Ebalunode cc: namd-l@ks.uiuc.edu Subject: Re: namd-l: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 In-Reply-To: <200401021204.41329.jebalunode@uh.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, Please make this change in your charm++ config file at: charm/src/arch/mpi-linux-ia64/cc-ecc.sh add -fpic as one command line option to both c and c++ compiler, i.e. change line: CMK_CC="ecc $CMK_INCDIR " to CMK_CC="ecc -fpic $CMK_INCDIR " also CMK_CXX="ecpc $CMK_INCDIR " to CMK_CXX="ecpc -fpic $CMK_INCDIR " please let me know if this fix the compilation and I will commit the change into cvs. Gengbin On Fri, 2 Jan 2004, Jerry Ebalunode wrote: > Hi Gengbin, > Sorry it took so long to get back to you. Well here is output during the > compilation charm++ using intel c+ compiler version 8 > [jebalunode@mckinley charm]$ ./build charm++ mpi-linux-ia64 ecc > Selected Compiler: ecc > Selected Options: > Copying src/scripts/Makefile to mpi-linux-ia64-ecc/tmp > Soft-linking over bin > Soft-linking over lib > Soft-linking over lib_so > Soft-linking over include > Soft-linking over tmp > Generating mpi-linux-ia64-ecc/tmp/conv-mach-pre.sh > Performing 'make charm++ OPTS=' in mpi-linux-ia64-ecc/tmp > make headerlinks > make[1]: Entering directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > ../bin/charmc -native -language c++ -cp ../bin/ -o charmxi xi-main.o > xi-symbol.o xi-grammar.tab.o xi-scan.o xi-util.o sdag-globals.o > CSdagConstruct.o CEntry.o > ../bin/charmc -intrinsic -build-shared ckcallback.ci > ../bin/charmc -intrinsic -build-shared ckmarshall.ci > ../bin/charmc -intrinsic -build-shared ckarray.ci > ../bin/charmc -intrinsic -build-shared cklocation.ci > ../bin/charmc -intrinsic -build-shared ckreduction.ci > ../bin/charmc -intrinsic -build-shared ckarrayreductionmgr.ci > ../bin/charmc -intrinsic -build-shared tempo.ci > ../bin/charmc -intrinsic -build-shared waitqd.ci > ../bin/charmc -intrinsic -build-shared ckfutures.ci > ../bin/charmc -intrinsic -build-shared ckcheckpoint.ci > ../bin/charmc -intrinsic -build-shared LBDatabase.ci > ../bin/charmc -intrinsic -build-shared CentralLB.ci > ../bin/charmc -intrinsic -build-shared ComboCentLB.ci > ../bin/charmc -intrinsic -build-shared NullLB.ci > ../bin/charmc -intrinsic -build-shared RandCentLB.ci > ../bin/charmc -intrinsic -build-shared RecBisectBfLB.ci > ../bin/charmc -intrinsic -build-shared BaseLB.ci > ../bin/charmc -intrinsic -build-shared MetisLB.ci > ../bin/charmc -intrinsic -build-shared DummyLB.ci > ../bin/charmc -intrinsic -build-shared RefineLB.ci > ../bin/charmc -intrinsic -build-shared RefineCommLB.ci > ../bin/charmc -intrinsic -build-shared OrbLB.ci > ../bin/charmc -intrinsic -build-shared GreedyLB.ci > ../bin/charmc -intrinsic -build-shared NborBaseLB.ci > ../bin/charmc -intrinsic -build-shared NeighborLB.ci > ../bin/charmc -intrinsic -build-shared NeighborCommLB.ci > ../bin/charmc -intrinsic -build-shared WSLB.ci > ../bin/charmc -intrinsic -build-shared GreedyRefLB.ci > ../bin/charmc -intrinsic -build-shared RandRefLB.ci > ../bin/charmc -intrinsic -build-shared GreedyCommLB.ci > ../bin/charmc -intrinsic -build-shared Comm1LB.ci > ../bin/charmc -intrinsic -build-shared EveryLB.ci > ../bin/charmc -intrinsic -build-shared charisma.ci > ../bin/charmc -intrinsic -build-shared trace-summary.ci > ../bin/charmc -intrinsic -build-shared BlueGene.ci > Soft-linking headers... > make[1]: [headerlinks] Error 1 (ignored) > touch headerlinks > make[1]: Leaving directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > touch basics > make charm-target > make[1]: Entering directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > make headerlinks > make[2]: Entering directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > make[2]: `headerlinks' is up to date. > make[2]: Leaving directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > touch basics > make QuickThreads/libqt.a > make[2]: Entering directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > make[2]: `QuickThreads/libqt.a' is up to date. > make[2]: Leaving directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > make converse-target > make[2]: Entering directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > ../bin/charmc -build-shared -c -I. convcore.c > convcore.c(2004): warning #266: function declared implicitly > CmiTimerInit(); > ^ > > ../bin/charmc -build-shared -c -I. conv-conds.c > ../bin/charmc -build-shared -c -I. queueing.c > ../bin/charmc -build-shared -c -I. msgmgr.c > ../bin/charmc -build-shared -c -I. cpm.c > ../bin/charmc -build-shared -c -I. cpthreads.c > ../bin/charmc -build-shared -c -I. futures.c > ../bin/charmc -build-shared -c -I. cldb.c > ../bin/charmc -build-shared -c -I. topology.C > ../bin/charmc -build-shared -c -I. random.c > ../bin/charmc -build-shared -c -I. debug-conv.c > ../bin/charmc -build-shared -c -I. generate.c > ../bin/charmc -build-shared -c -I. edgelist.c > edgelist.c(58): warning #1193: standard requires that parameter "x" be given a > type by a subsequent declaration ("int" assumed) > int edgeExists(x,y) > ^ > > edgelist.c(58): warning #1193: standard requires that parameter "y" be given a > type by a subsequent declaration ("int" assumed) > int edgeExists(x,y) > ^ > > ../bin/charmc -build-shared -c -I. conv-ccs.c > ccs-server.c(311): warning #266: function declared implicitly > if (isxdigit(key[0]) && isxdigit(key[1])) > ^ > > ccs-server.c(353): warning #167: argument of type "unsigned int *far" is > incompatible with parameter of type "int *far" > ccs_server_fd=skt_server(&port); > ^ > > ccs-server.c(416): warning #167: argument of type "unsigned int *far" is > incompatible with parameter of type "int *far" > fd=skt_accept(ccs_server_fd,&ip,&port); > ^ > > ../bin/charmc -build-shared -c -I. ccs-builtins.C > ../bin/charmc -build-shared -c -I. traceCore.C > traceCoreAPI.h(8): warning #380: linkage specification is incompatible with > previous "Cpv__traceCoreOn_" (declared at line 20 of "traceCore.h") > CpvExtern(int,_traceCoreOn); > ^ > > ../bin/charmc -build-shared -c -I. traceCoreCommon.C > traceCoreAPI.h(8): warning #380: linkage specification is incompatible with > previous "Cpv__traceCoreOn_" (declared at line 20 of "traceCore.h") > CpvExtern(int,_traceCoreOn); > ^ > > ../bin/charmc -build-shared -c -I. converseProjections.C > ../bin/charmc -build-shared -c -I. machineProjections.C > ../bin/charmc -build-shared -c -I. quiescence.c > ../bin/charmc -build-shared -c -I. isomalloc.c > ../bin/charmc -build-shared -c -I. global-nop.c > ../bin/charmc -build-shared -o ../lib/libconv-core.a convcore.o conv-conds.o > queueing.o msgmgr.o cpm.o cpthreads.o futures.o cldb.o topology.o random.o > debug-conv.o generate.o edgelist.o conv-ccs.o ccs-builtins.o traceCore.o > traceCoreCommon.o converseProjections.o machineProjections.o quiescence.o > isomalloc.o global-nop.o > Warning: creating ../lib_so/libconv-core.so > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > keys_inactive > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > keys_inactive > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_current_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_current_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_current_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_current_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol keys_active > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_current_ > /usr/bin/ld: cpthreads.o: @gprel relocation against dynamic symbol > Csv_CtvOffsCpthread_errcode_ > Fatal Error by charmc in > directory /tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp > Command icc -L/opt/scali/lib -lmpi -o ../lib_so/libconv-core.so -shared > -L/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/lib_so > convcore.o conv-conds.o queueing.o msgmgr.o cpm.o cpthreads.o futures.o > cldb.o topology.o random.o debug-conv.o generate.o edgelist.o conv-ccs.o > ccs-builtins.o traceCore.o traceCoreCommon.o converseProjections.o > machineProjections.o quiescence.o isomalloc.o global-nop.o returned error > code 1 > charmc exiting... > make[2]: *** [../lib/libconv-core.a] Error 1 > make[2]: Leaving directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > make[1]: *** [converse] Error 2 > make[1]: Leaving directory > `/tlccs2a/home/briggs/jebalunode/src/NAMD_2.5_Source/charm/mpi-linux-ia64-ecc/tmp' > make: *** [charm++] Error 2 > > On Wednesday 31 December 2003 01:25 pm, Gengbin Zheng wrote: > > I don't have access to Intel C++ compilers v8.0 on IA64. Could you copy me > > the compile error messages? > > > > Gengbin > > > > On Wed, 31 Dec 2003, Jerry Ebalunode wrote: > > > Hi, > > > I would like to know if Charm++ and then NAMD can be built using the new > > > intel C++ compiler version 8.0 on an IA64 arch. I already tried this on > > > the charm++ source code that was provided along with the namd ver2.5., > > > with no succes in compling charm++ for mpi-linux-ia64. > > > > > > On Wednesday 31 December 2003 11:59 am, Gengbin Zheng wrote: > > > > Oops, forgot to mention, you need to recompile Linux version of NAMD > > > > from scratch also. The pre-compiled version is not compatiable with the > > > > latest CVS version due to my recent changes in structure layout. Also, > > > > the pre-compiled version is built with Intel C++ compiler which I have > > > > not tested the compatibility with Win32 VC++ yet. So I would suggest > > > > going with gcc on Linux before I tested it with Intel C++. > > > > > > > > Since I don't know which verison of Linux you are running, I don't know > > > > how to make pre-compiled binary for you. But compiling for Linux is > > > > fairely easy, check out: > > > > http://www.ks.uiuc.edu/Research/namd/development.html > > > > Please download both Charm++ and NAMD source from the two different CVS > > > > servers. > > > > > > > > I myself rarely use tcl and plugins features (being a mostly Charm++ > > > > developer). Based on my limited knowledge, tcl is used to enable > > > > scripting features (so you can write tcl scripts in config file), and > > > > plugins tools are from VMD's Plugins to enable trajectory analysis. The > > > > NAMD user manual should have more detailed information. > > > > > > > > Gengbin > > > > > > > > On Wed, 31 Dec 2003, Gadi Oron wrote: > > > > > On Wed, 2003-12-31 at 02:05, Gengbin Zheng wrote: > > > > > > Hi, > > > > > > > > > > > > Please find the NAMD binary compiled with Windows VC++ 6.0 at: > > > > > > http://www.ks.uiuc.edu/~gzheng/NAMD_Win32-i686.zip > > > > > > > > > > Thank you, but still no luck... > > > > > I manage to start NAMD alone on a Win2K node and on Linux node, > > > > > so probably my nodelist is Ok. But together I get either: > > > > > > > > > > Info: SUMMARY OF PARAMETERS: > > > > > Info: 180 BONDS > > > > > Info: 442 ANGLES > > > > > Info: 534 DIHEDRAL > > > > > Info: 50 IMPROPER > > > > > Info: 91 VDW > > > > > Info: 0 VDW_PAIRS > > > > > Charmrun: error on request socket-- > > > > > Error on socket recv! > > > > > > > > > > when the Linux box is first in the nodelist and: > > > > > > > > > > Charmrun> node programs all connected > > > > > ------------- Processor 1 Exiting: Caught Signal ------------ > > > > > Signal: segmentation violation > > > > > Suggestion: Try running with '++debug', or linking with '-memory > > > > > paranoid'. > > > > > Fatal error on PE 1> segmentation violation > > > > > > > > > > when the order is inverted. > > > > > > > > > > I am using charmd compiled from the last source and NAMD 2.5 from > > > > > the pre-compiled binaries for linux and your Windows executables. > > > > > > > > > > Any idea? > > > > > > > > > > Best regards. > > > > > > > > > > P.S. It is not really explained what "plugins" and "tcl" libraries > > > > > are needed for... Could you give me a hint on that? > > > > > -- > > > > > ================= Gadi ORON, PhD -o- Proteologics > > > > > ====================== ========== gadi/at/proteologics.com ========== > > > > > +972 8 9475666 ========== The questions remain the same. The answers > > > > > are eternally variable. > > > > > > -- > > > Cheers, > > > > > > Jerry Ebalunode > > > Graduate Research Assistant > > > RM 402F Houston Science Center > > > Phone: 713-743-8367 > > > Dept. of Biology and Biochemistry > > > University of Houston. > > > 4800 Calhoun Road > > > Houston, TX 77204 > > -- > Cheers, > > Jerry Ebalunode > Graduate Research Assistant > RM 402F Houston Science Center > Phone: 713-743-8367 > Dept. of Biology and Biochemistry > University of Houston. > 4800 Calhoun Road > Houston, TX 77204 > From owner-namd-l@rama.ks.uiuc.edu Fri Jan 2 17:46:00 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i02Nk0tX020258 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 2 Jan 2004 17:46:00 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i02Nk0Fx020257 for namd-l-outgoing; Fri, 2 Jan 2004 17:46:00 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from lulu.it.northwestern.edu (lulu.it.northwestern.edu [129.105.16.54]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i02NjxtW020253 for ; Fri, 2 Jan 2004 17:45:59 -0600 (CST) Received: (from mailnull@localhost) by lulu.it.northwestern.edu (8.12.10/8.12.10) id i02Njx0g014681 for ; Fri, 2 Jan 2004 17:45:59 -0600 (CST) Received: from northwestern.edu (gallium.theory.northwestern.edu [129.105.55.26]) by lulu.it.northwestern.edu via smap (V2.0) id xma014550; Fri, 2 Jan 04 17:45:51 -0600 Message-ID: <3FF602AE.5070103@northwestern.edu> Date: Fri, 02 Jan 2004 17:45:50 -0600 From: Hyonseok Hwang User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en, ko MIME-Version: 1.0 To: namd-l@ks.uiuc.edu Subject: namd-l: question on the coordinates of hydrogen atoms Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hellow, Now I have PDB file which include all the atoms' coordiates even hydrogen atoms' coordinates. As a result, I don't want use 'guesscoord' command when I make a NAMD PDB file and 'PSF' file. But, if I don't use the command, the coordinates of hydrogen atoms are just missing in the NAMD PDB file. So my question is whether or not there is a way to keep the original coordiates of hydrogen atoms when we make a NAMD PDB file. Thanks a lot! -Hyonseok From owner-namd-l@rama.ks.uiuc.edu Sat Jan 3 05:19:05 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i03BJ5tX001639 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sat, 3 Jan 2004 05:19:05 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i03BJ54J001638 for namd-l-outgoing; Sat, 3 Jan 2004 05:19:05 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from mail.ccnu.edu.cn ([202.114.32.3]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i03BIrtW001615 for ; Sat, 3 Jan 2004 05:18:55 -0600 (CST) Received: (eyou send program); Sat, 03 Jan 2004 19:18:48 +0800 Message-ID: <273128728.28458@mail.ccnu.edu.cn> Received: from 202.114.34.252 by 202.114.32.3 with HTTP; Sat, 03 Jan 2004 19:18:48 +0800 X-WebMAIL-MUA: [202.114.34.252] From: "" To: namd-l@ks.uiuc.edu Date: Sat, 03 Jan 2004 19:18:48 +0800 Reply-To: "" Subject: namd-l: different result when I run the same *.conf file many times. Content-Type: text/plain Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Dear sir, I want to do MD for an enzyme-ligand system to study the coordinate number of zinc ion of the enzyme. However I find I get different result when I run the same *.conf file many times. Some results are in good agreement with experimental X-ray data, and some are not. I am so surprised with it. Would you like to tell me what's wrong with it? Thank you! From owner-namd-l@rama.ks.uiuc.edu Sat Jan 3 21:44:13 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i043iDtX016490 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sat, 3 Jan 2004 21:44:13 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i043iDSe016489 for namd-l-outgoing; Sat, 3 Jan 2004 21:44:13 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from gradea.uci.edu (grad-ea-1.nacs.uci.edu [128.200.84.61]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i043iCtX016484 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sat, 3 Jan 2004 21:44:12 -0600 (CST) Received: from gradea.uci.edu (localhost.localdomain [127.0.0.1]) by gradea.uci.edu (8.12.8/8.11.6) with ESMTP id i043i6lL003940 for ; Sat, 3 Jan 2004 19:44:06 -0800 Received: from localhost (jfreites@localhost) by gradea.uci.edu (8.12.8/8.12.8/Submit) with ESMTP id i043i5M5003936 for ; Sat, 3 Jan 2004 19:44:05 -0800 Date: Sat, 3 Jan 2004 19:44:05 -0800 (PST) From: Juan Alfredo Freites To: namd-l@ks.uiuc.edu Subject: namd-l: flexible cell Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hello, I sent this message over the holidays, so I thought that I could post it again now when there are more folks around. Thanks. Hello, I'm doing a simulation using a flexible cell and constant surface tension. I keep getting this message: FATAL ERROR: Periodic cell has become too small for original patch grid! Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation. What I have done is restart the simulation every time I get the error, the simulation runs for over 100K steps and it gives me the error again. I thought about giving a non zero margin but there are not details in the manual as to which should be the magnitude of it. Any thoughts? thanks. -- J. Alfredo Freites Department of Physics University of California, Irvine Irvine, CA 92697-4575 (949) 824-9921 From owner-namd-l@rama.ks.uiuc.edu Sat Jan 3 22:01:52 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i0441qtX016780 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sat, 3 Jan 2004 22:01:52 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i0441qrN016779 for namd-l-outgoing; Sat, 3 Jan 2004 22:01:52 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from marcy.nas.nasa.gov (marcy.nas.nasa.gov [129.99.113.17]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i0441ptW016775 for ; Sat, 3 Jan 2004 22:01:51 -0600 (CST) Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7p1+Sun/8.11.7/NAS-6n) with ESMTP id i0441jW06675 for ; Sat, 3 Jan 2004 20:01:45 -0800 (PST) Date: Sat, 3 Jan 2004 20:01:45 -0800 (PST) From: Ioana Cozmuta To: namd-l@ks.uiuc.edu Subject: namd-l: SMD force Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, Happy New Year to everybody and lots of successful simulations with NAMD in 2004! I have a short question related to SMD output. The manual says that at every SMD step the program writes out 1. the current timestep, 2. the current position of the center of mass of the restrained atoms and 3. the current force applied to the center of mass (pN). It is not clear to me what exactly does "current force applied to the center of mass" means: a. force due to dragging of the atoms with velocity v via a harmonical constraint k b. force due to the interaction with the surroundings c. both dragging force and interaction with the surroundings I want to use the information in the output to calculate only the component due to the interaction between the restrained atoms and the surroundings. Thanks in advance for your answer, Ioana From owner-namd-l@rama.ks.uiuc.edu Sun Jan 4 16:23:31 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i04MNVtX008056 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sun, 4 Jan 2004 16:23:31 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i04MNVKT008055 for namd-l-outgoing; Sun, 4 Jan 2004 16:23:31 -0600 (CST) X-Authentication-Warning: rama.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 [130.126.120.65]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i04MNStY008050 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT); Sun, 4 Jan 2004 16:23:28 -0600 (CST) Date: Sun, 4 Jan 2004 16:23:27 -0600 (CST) From: Gengbin Zheng To: Gadi Oron cc: namd-l@ks.uiuc.edu, Subject: Re: namd-l: Charm++ nodelist commands In-Reply-To: <1073220303.17244.18.camel@pooh.proteologics.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk On Sun, 4 Jan 2004, Gadi Oron wrote: > Hello again... > > On Fri, 2004-01-02 at 20:09, Gengbin Zheng wrote: > > > > > Another question: is it possible to set process priority (nice level) > > > > > for NAMD node programs? > > > > > > > > > > > > > No. It can be implemented but not for windows I guess. > > > > > > > > You can now. This has been implemented in Charm++ CVS server. > > It is only for non windows versions. > > Thank you very much, this option is very helpful! > > I believe though that with Cygwin the your implementation should be > functional. (The nice command exists). > ok, Windows version of setting process priority (using SetPriorityClass Win32 call) is also implemented. It should work for both Cygwin(gcc) and pure windows(visual c++) binary. Since windows does not support numeric nice level - it only has these 6 levels (from high to low), I had to do a mapping from +nice parameter value to the win priority levels: REALTIME_PRIORITY_CLASS <= -20 HIGH_PRIORITY_CLASS -20 - -10 ABOVE_NORMAL_PRIORITY_CLASS -10 - 0 NORMAL_PRIORITY_CLASS 0 BELOW_NORMAL_PRIORITY_CLASS 0 - 10 IDLE_PRIORITY_CLASS > 10 Note that not every Windows supports ABOVE_NORMAL_PRIORITY_CLASS and BELOW_NORMAL_PRIORITY_CLASS for example win95/ME. So when not supported, the value will be overtaken by corresponding IDLE_PRIORITY_CLASS or HIGH_PRIORITY_CLASS. Again, you may need administrator privilege to set high priorities. Same as explained in previous email, to set priority nice level, you can: 1. ./charmrun +p4 ./pgm +nice -5 to set nice level to -5 (higher priority) for all 4 node processes. This works for *all* charm/NAMD version now. 2. put ++nice in a nodelist file: group main host host-1 ++nice 2 host host-2 ++nice -2 This only works for net-* version when nodelist is read. My test shows that setting very high priority under windows do have noticeable good impact in the execution time. The latest NAMD win32/VC++ binary for testing is now at: http://www.ks.uiuc.edu/~gzheng/NAMD_Win32-i686.zip It is compiled with Charm++/net-win32 with -O -DCMK_OPTIMIZE and NAMD/Win32-i686-MSVC with tcl and plugins libraries. The VC++ I was using to compile the binary donot have BELOW_NORMAL_PRIORITY_CLASS and ABOVE_NORMAL_PRIORITY_CLASS defined, so these two priorities are not supported in this binary. (for cross linux/windows clusters usage, please note that you need exact same charm++ source code from cvs, also with exact *Charm++ defined macros* - that is with or without -DCMK_OPTIMIZE, binaries with CMK_OPTIMIZE is not compatible with the one compiled without the flag when running cross the platforms.) Gengbin From owner-namd-l@rama.ks.uiuc.edu Sun Jan 4 18:09:59 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i0509stX010310 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sun, 4 Jan 2004 18:09:55 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i0509sDG010309 for namd-l-outgoing; Sun, 4 Jan 2004 18:09:54 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from ALPHA9.ITS.MONASH.EDU.AU (alpha9.its.monash.edu.au [130.194.1.9]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i0509rtW010305 for ; Sun, 4 Jan 2004 18:09:54 -0600 (CST) Received: from localhost ([130.194.13.81]) by vaxh.its.monash.edu.au (PMDF V5.2-31 #39306) with ESMTP id <01L51CPGOSYW8ZZRWD@vaxh.its.monash.edu.au> for namd-l@ks.uiuc.edu; Mon, 5 Jan 2004 10:55:17 +1100 Received: from kapow.its.monash.edu.au (localhost.its.monash.edu.au [127.0.0.1]) by localhost (Postfix) with ESMTP id 2BC4D1B0002 for ; Mon, 05 Jan 2004 10:55:17 +1100 (EST) Received: from orion.vcp.monash.edu.au (orion.vcp.monash.edu.au [130.194.229.65]) by kapow.its.monash.edu.au (Postfix) with ESMTP id 14E36124003 for ; Mon, 05 Jan 2004 10:55:17 +1100 (EST) Received: from orion.vcp.monash.edu.au (localhost [127.0.0.1]) by orion.vcp.monash.edu.au (SGI-8.12.5/8.12.5) with ESMTP id i04NtG0a065630 for ; Mon, 05 Jan 2004 10:55:16 +1100 (EDT) Received: from localhost (david@localhost) by orion.vcp.monash.edu.au (SGI-8.12.5/8.12.5/Submit) with ESMTP id i04NtFDr065467 for ; Mon, 05 Jan 2004 10:55:16 +1100 (EDT) Date: Mon, 05 Jan 2004 10:55:15 +1100 From: David Chalmers Subject: namd-l: NAMD for Opteron? X-X-Sender: david@orion.vcp.monash.edu.au To: namd-l@ks.uiuc.edu Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT X-Authentication-warning: orion.vcp.monash.edu.au: david owned process doing -bs Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Dear NAMD Developers, A couple of quick questions. Do you have a version of NAMD for Opteron/Linux? Do you expect that NAMD will benefit from being compiled for 64 bit CPUs? Regards, David _____________________________________________________________________________ David Chalmers Lab: 9903 9110 Victorian College of Pharmacy Fax: 9903 9582 381 Royal Pde, Parkville, Vic 3053 Australia David.Chalmers@vcp.monash.edu.au _____________________________________________________________________________ From owner-namd-l@rama.ks.uiuc.edu Sun Jan 4 18:32:24 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i050WOtX010947 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sun, 4 Jan 2004 18:32:24 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i050WOrx010946 for namd-l-outgoing; Sun, 4 Jan 2004 18:32:24 -0600 (CST) X-Authentication-Warning: rama.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 [130.126.120.65]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i050WLtY010931 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT); Sun, 4 Jan 2004 18:32:21 -0600 (CST) Date: Sun, 4 Jan 2004 18:32:21 -0600 (CST) From: Gengbin Zheng To: David Chalmers cc: namd-l@ks.uiuc.edu Subject: Re: namd-l: NAMD for Opteron? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, Yes, you can build charm++/namd2 on Opteron: compile charm++ with opteron build options: ./build charm++ net-linux opteron -O -DCMK_OPTIMIZE and build namd2 with: config ... Linux-amd64-g++ We don't have Opteron machine in our lab, but I heard from other people using it. My impression is that compiling with 64 bits did not improve the performance, it may be even a little bit slower. Gengbin On Mon, 5 Jan 2004, David Chalmers wrote: > Dear NAMD Developers, > > A couple of quick questions. Do you have a version of NAMD for > Opteron/Linux? Do you expect that NAMD will benefit from being compiled > for 64 bit CPUs? > > Regards, > > David > > _____________________________________________________________________________ > > David Chalmers Lab: 9903 9110 > Victorian College of Pharmacy Fax: 9903 9582 > 381 Royal Pde, Parkville, Vic 3053 > Australia David.Chalmers@vcp.monash.edu.au > _____________________________________________________________________________ > From owner-namd-l@rama.ks.uiuc.edu Sun Jan 4 20:05:26 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i0525QtX013112 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sun, 4 Jan 2004 20:05:26 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i0525Qpw013111 for namd-l-outgoing; Sun, 4 Jan 2004 20:05:26 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from ustc.edu ([218.22.21.7]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i0525MtW013107 for ; Sun, 4 Jan 2004 20:05:24 -0600 (CST) Received: (qmail 15917 invoked by uid 0); 5 Jan 2004 02:05:25 -0000 Received: from unknown (HELO localhost) ([218.22.21.7]) (envelope-sender ) by 0 (magicmail-2.1) with SMTP for ; 5 Jan 2004 02:05:25 -0000 From: "li" To: "namd-l" Subject: namd-l: Warning: 8 margin violations Date: Mon, 05 Jan 2004 10:05:25 CST 0008 X-Mailer: MagicMail WebMail X-Priority: 3 Reply-To: zlee@ustc.edu Message-ID: <273128728.28458@mail.ccnu.edu.cn@magicmail> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="MagicMail--268325535be68e069e1ad52b128834299d34fbbfb" Content-Transfer-Encoding: base64 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk This is a MIME encoded message. --MagicMail--268325535be68e069e1ad52b128834299d34fbbfb Content-Type: text/plain; charset=iso-8895-1 Content-Transfer-Encoding: base64 aGksZXZlcnlvbmUgOg0Kd2hvIGNhbiB0ZWxsIG1lIGhvdyB0byBkZWFsIHdpdGggdGhpcyBraW5k IG9mIHdhcm5pbmc6DQoiV2FybmluZzogOCBtYXJnaW4gdmlvbGF0aW9ucyBkZXRlY3RlZCBkdXJp bmcgdGltZXN0ZXAgMzYxMDEuIg0KIldhcm5pbmc6IDc0NiBtYXJnaW4gdmlvbGF0aW9ucyBkZXRl Y3RlZCBzaW5jZSBwcmV2aW91cyBlbmVyZ3kgb3V0cHV0Ig0KSSBjYW4gbm90IHVuZGVyc3RhbmQg dGhlIG1lYW5pbmcgb2YgTUFSR0lOIGluIE5BTUQgLg0KVGhhbmtzIGEgbG90ICEhIQotLQ0KVVNU QyBBbHVtbmkgRW1haWwgU3lzdGVtIAoK --MagicMail--268325535be68e069e1ad52b128834299d34fbbfb Content-Type: text/html Content-Transfer-Encoding: base64 PEhUTUw+PGJvZHk+PFA+aGksZXZlcnlvbmUgOjwvUD4NCjxQPndobyBjYW4gdGVsbCBtZSBob3cg dG8gZGVhbCB3aXRoIHRoaXMga2luZCBvZiB3YXJuaW5nOjwvUD4NCjxQPiJXYXJuaW5nOiA4IG1h cmdpbiB2aW9sYXRpb25zIGRldGVjdGVkIGR1cmluZyB0aW1lc3RlcCAzNjEwMS4iPC9QPg0KPFA+ Ildhcm5pbmc6IDc0NiBtYXJnaW4gdmlvbGF0aW9ucyBkZXRlY3RlZCBzaW5jZSBwcmV2aW91cyBl bmVyZ3kgb3V0cHV0IjwvUD4NCjxQPkkgY2FuIG5vdCB1bmRlcnN0YW5kIHRoZSBtZWFuaW5nIG9m IE1BUkdJTiBpbiBOQU1EIC48L1A+DQo8UD5UaGFua3MgYSBsb3QgISEhPC9QPjwvYm9keT48L0hU TUw+PGJyPgotLQ0KVVNUQyBBbHVtbmkgRW1haWwgU3lzdGVtIDxicj4KPGJyPgo= --MagicMail--268325535be68e069e1ad52b128834299d34fbbfb-- From owner-namd-l@rama.ks.uiuc.edu Sun Jan 4 23:18:45 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i055IjtX017162 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sun, 4 Jan 2004 23:18:45 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i055Ijsn017161 for namd-l-outgoing; Sun, 4 Jan 2004 23:18:45 -0600 (CST) X-Authentication-Warning: rama.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 [130.126.120.65]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i055IgtY017157 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT); Sun, 4 Jan 2004 23:18:42 -0600 (CST) Date: Sun, 4 Jan 2004 23:18:42 -0600 (CST) From: Gengbin Zheng To: Gadi Oron cc: namd-l@ks.uiuc.edu Subject: Re: namd-l: Charm++ nodelist commands In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, Please find the charm++ and NAMD source files I used to compile the Windows binary at: http://www.ks.uiuc.edu/~gzheng/charm.tgz http://www.ks.uiuc.edu/~gzheng/namd2.tgz (same as in the cvs version today) Use this same source for Linux, and please don't download from the Charm++ cvs server. Build charm++ for Linux with this command line: ./build charm++ net-linux -O -DCMK_OPTIMIZE Keep in mind that the code in cvs server is changing every day recently for a major Charm++ release soon coming in about a month. I can not guarantee the cross platform compatibility to my previous namd2/win32 binary for arbitary cvs snapshot. So I figure it is better to give you the snapshot I used for my testing. The tcl and plugins are optional. You don't have to compile with them if you don't need them. Fftw, however, is often found essential. Gengbin On Sun, 4 Jan 2004, Gengbin Zheng wrote: > > On Sun, 4 Jan 2004, Gadi Oron wrote: > > > Hello again... > > > > On Fri, 2004-01-02 at 20:09, Gengbin Zheng wrote: > > > > > > Another question: is it possible to set process priority (nice > level) > > > > > > for NAMD node programs? > > > > > > > > > > > > > > > > No. It can be implemented but not for windows I guess. > > > > > > > > > > > You can now. This has been implemented in Charm++ CVS server. > > > It is only for non windows versions. > > > > Thank you very much, this option is very helpful! > > > > I believe though that with Cygwin the your implementation should be > > functional. (The nice command exists). > > > > ok, Windows version of setting process priority (using SetPriorityClass > Win32 call) is also implemented. It should work for both Cygwin(gcc) and > pure windows(visual c++) binary. > > Since windows does not support numeric nice level - it only > has these 6 levels (from high to low), I had to do a mapping from +nice > parameter value to the win priority levels: > > REALTIME_PRIORITY_CLASS <= -20 > HIGH_PRIORITY_CLASS -20 - -10 > ABOVE_NORMAL_PRIORITY_CLASS -10 - 0 > NORMAL_PRIORITY_CLASS 0 > BELOW_NORMAL_PRIORITY_CLASS 0 - 10 > IDLE_PRIORITY_CLASS > 10 > > Note that not every Windows supports ABOVE_NORMAL_PRIORITY_CLASS and > BELOW_NORMAL_PRIORITY_CLASS for example win95/ME. So when not supported, > the value will be overtaken by corresponding IDLE_PRIORITY_CLASS or > HIGH_PRIORITY_CLASS. > Again, you may need administrator privilege to set high priorities. > > Same as explained in previous email, to set priority nice level, you can: > 1. ./charmrun +p4 ./pgm +nice -5 > to set nice level to -5 (higher priority) for all 4 node processes. > This works for *all* charm/NAMD version now. > 2. put ++nice in a nodelist file: > group main > host host-1 ++nice 2 > host host-2 ++nice -2 > This only works for net-* version when nodelist is read. > > My test shows that setting very high priority under windows do have > noticeable good impact in the execution time. > > The latest NAMD win32/VC++ binary for testing is now at: > > http://www.ks.uiuc.edu/~gzheng/NAMD_Win32-i686.zip > > It is compiled with Charm++/net-win32 with -O -DCMK_OPTIMIZE > and NAMD/Win32-i686-MSVC with tcl and plugins libraries. > > The VC++ I was using to compile the binary donot have > BELOW_NORMAL_PRIORITY_CLASS and ABOVE_NORMAL_PRIORITY_CLASS defined, so > these two priorities are not supported in this binary. > > (for cross linux/windows clusters usage, please note that you need exact > same charm++ source code from cvs, also with exact *Charm++ defined > macros* - that is with or without -DCMK_OPTIMIZE, binaries with > CMK_OPTIMIZE is not compatible with the one compiled without the flag > when running cross the platforms.) > > Gengbin > > > > > Gengbin Zheng ============ (217)244-3667 (o) gzheng@uiuc.edu zhenggb@acm.org http://www.ks.uiuc.edu/~gzheng/personal.html From owner-namd-l@rama.ks.uiuc.edu Mon Jan 5 00:31:24 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i056VOtX018706 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Mon, 5 Jan 2004 00:31:24 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i056VO6n018705 for namd-l-outgoing; Mon, 5 Jan 2004 00:31:24 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from jhuml3.jhu.edu (jhuml3.jhu.edu [128.220.2.66]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i056VNtW018701 for ; Mon, 5 Jan 2004 00:31:24 -0600 (CST) Received: from jhuml3.jhu.edu (jhuml3.jhu.edu [128.220.2.66]) by jhuml3.jhu.edu (PMDF V6.2-X17 #30840) with SMTP id <0HR000JFL7FZSZ@jhuml3.jhu.edu> for namd-l@ks.uiuc.edu; Mon, 05 Jan 2004 01:31:23 -0500 (EST) Received: from jhuml3.jhu.edu ([128.220.2.66]) by jhuml3.jhu.edu (SAVSMTP 3.1.0.29) with SMTP id M2004010501312312927 for ; Mon, 05 Jan 2004 01:31:23 -0500 Received: from jhumail.jhu.edu (jhem1.jhmi.edu [162.129.8.22]) by jhuml3.jhu.edu (PMDF V6.2-X17 #30840) with ESMTP id <0HR000JG87GBSZ@jhuml3.jhu.edu> for namd-l@ks.uiuc.edu; Mon, 05 Jan 2004 01:31:23 -0500 (EST) Received: from [151.196.116.46] by jhumail.jhu.edu (mshttpd); Mon, 05 Jan 2004 01:37:05 -0500 Date: Mon, 05 Jan 2004 01:37:05 -0500 From: AMIT PALIWAL Subject: namd-l: alchemical free energy perturbation To: namd-l@ks.uiuc.edu Message-id: <31dd233229.3322931dd2@jhumail.jhu.edu> MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.17 (built Jun 23 2003) Content-type: multipart/mixed; boundary=--50c0518d6b643cbb Content-language: en X-Accept-Language: en Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk This is a multi-part message in MIME format. ----50c0518d6b643cbb Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit Hi, I want to calculate the free energy change of growing a 3.0 ang. radius LJ particle in water. I tried dual-topolgy method outlined in tutorial on NAMD site but did not give expected free energy values. Is there any way to 'grow/shrink' rather than going from lambda=0 (nothing) to lambda =1 (full partcle)? Are they the same? I have also attached the config file, part of the fep file (system.fep). The system is a LJ particle with 1000 water molecules. thanks, Amit. PS: CMT is the atom type of the LJ particle that I have defined. ----50c0518d6b643cbb Content-Type: text/plain Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename=growth.namd I1Byb2R1Y3Rpb24gTkFNRCBjb25maWcgZmlsZSBmb3IgY29tYmluZWJveAoKdGVtcGVyYXR1 cmUgMjk4LjAKCiNjb29yZHMgc3RydWN0dXJlIGFuZCB2ZWxvY2l0aWVzCnN0cnVjdHVyZSAg ICAgICAgICAgY29tYmluZS5wc2YKY29vcmRpbmF0ZXMgICAgICAgICBjb21iaW5lLmNvb3IK CiNpbnRlcmFjdGlvbnMKcGFyYVR5cGVDaGFybW0gICAgICAgb24KcGFyYW1ldGVycyAgICAg ICAgICAgcGFyX2FsbDI3X3Byb3RfbGlwaWQuaW5wCmV4Y2x1ZGUgICAgICAgICAgICAgIHNj YWxlZDEtNAoxLTRzY2FsaW5nICAgICAgICAgICAxLjAKc3dpdGNoaW5nICAgICAgICAgICAg b24Kc3dpdGNoZGlzdCAgICAgICAgICAgMTAKY3V0b2ZmICAgICAgICAgICAgICAgMTIKcGFp cmxpc3RkaXN0ICAgICAgICAgMTMuNQpzdGVwc3BlcmN5Y2xlICAgICAgICAyMAoKI25leHQg Zm9yIHNoYWtlCnJpZ2lkQm9uZHMgICAgICAgICAgIHdhdGVyCgpsYW5nZXZpbiBvbgpsYW5n ZXZpblRlbXAgMjk4LjAKbGFuZ2V2aW5EYW1waW5nIDEwLjAKbGFuZ2V2aW5IeWRyb2dlbiBv ZmYKCiMgcHJlc3N1cmUgY29udHJvbAoKbGFuZ2V2aW5QaXN0b24gb24KbGFuZ2V2aW5QaXN0 b250YXJnZXQgMS4wCmxhbmdldmluUGlzdG9ucGVyaW9kIDIwMApsYW5nZXZpblBpc3RvbmRl Y2F5ICAxMDAKbGFuZ2V2aW5QaXN0b250ZW1wICAgMjk4CgojcHJlc3N1cmUgYmF0aAojbmV4 dCBuZWVkZWQgd2hlbiBzaGFrZSdkCnVzZUdyb3VwUHJlc3N1cmUgICAgIHllcwoKI2tpbmQg b2YgY291cGxpbmcKI0JlcmVuZHNlblByZXNzdXJlICAgIG9uCiNCZXJlbmRzZW5QcmVzc3Vy ZVRhcmdldCAxLjAKI0JlcmVuZHNlblByZXNzdXJlQ29tcHJlc3NpYmlsaXR5IDAuMDAwMDUK I0JlcmVuZHNlblByZXNzdXJlUmVsYXhhdGlvblRpbWUgMjAwCiNCZXJlbmRzZW5QcmVzc3Vy ZUZyZXEgNAoKI3VzZSBwZXJpb2RpYyBib3VuZGFyeQpjZWxsQmFzaXNWZWN0b3IxICAgICAz MS40NTM0IDAuMCAwLjAKY2VsbEJhc2lzVmVjdG9yMiAgICAgMC4wIDMxLjQ1MzQgMC4wCmNl bGxCYXNpc1ZlY3RvcjMgICAgIDAuMCAwLjAgMzEuNDUzNApjZWxsT3JpZ2luICAgICAgICAg ICAwLjAgMC4wIDAuMAp3cmFwV2F0ZXIgICAgICAgICAgICBvbgoKI3VzZSBQTUUKUE1FICAg ICAgICAgICAgICAgICAgb24KUE1FR3JpZFNpemVYICAgICAgICAgMzIKUE1FR3JpZFNpemVZ ICAgICAgICAgMzIKUE1FR3JpZFNpemVaICAgICAgICAgMzIKZnVsbEVsZWN0RnJlcXVlbmN5 ICAgNAoKI3RpbWluZwpvdXRwdXR0aW1pbmcgICAgICAgICAwCnRpbWVzdGVwICAgICAgICAg ICAgIDEuMApudW1zdGVwcyAgICAgICAgICAgICA5NjAwMDIKCgoKI291dHB1dApiaW5hcnlv dXRwdXQgICAgICAgICBubwpvdXRwdXRuYW1lICAgICAgICAgICB0cmFqZWN0b3J5L3RpcDMK b3V0cHV0RW5lcmdpZXMgICAgICAgMTAwCgojc2F2ZSByZXN0YXJ0IGZpbGVzCmJpbmFyeXJl c3RhcnQgICAgICAgIG5vCnJlc3RhcnRuYW1lICAgICAgICAgIHRyYWplY3RvcnkvdGlwMwpy ZXN0YXJ0ZnJlcSAgICAgICAgICAxMDAwCnJlc3RhcnRzYXZlICAgICAgICAgIHllcwoKIyBG RVAKCmZlcCAJCW9uCmZlcEZpbGUgCXN5c3RlbS5mZXAKZmVwQ29sIAkJQgpmZXBPdXRGaWxl CXN5c3RlbS5mZXBvdXQKZmVwT3V0RnJlcQk1CkZlcEVxdWlsU3RlcHMgICAzMjAwCgoKIyBM T09QIE9WRVIgTEFNQkRBLVNUQVRFUyAtLSBUQ0wKCgpzZXQgc3RlcCAJMC4wMApzZXQgZHN0 ZXAJMC4wMQoKCndoaWxlIHskc3RlcCA8PSAxLjAwfSB7CgpmaXJzdHRpbWVzdGVwICAgMAps YW1iZGEgICAgICAgICAgJHN0ZXAKc2V0IHN0ZXAgW2V4cHIgJHN0ZXAgKyRkc3RlcF0KbGFt YmRhMiAgICAgICAgICRzdGVwCnJ1biA2NDAwCn0K ----50c0518d6b643cbb Content-Type: application/octet-stream Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename=system.fep UkVNQVJLIG9yaWdpbmFsIGdlbmVyYXRlZCBjb29yZGluYXRlIHBkYiBmaWxlDQpBVE9NICAg ICAgMSAgQ01UIE1URSAgICAgMSAgICAgICAwLjAwMCAgIDAuMDAwICAgMC4wMDAgIDEuMDAg IDEuMDAgICAgICBTT0xVDQpBVE9NICAgICAgMiAgT0gyIFRJUDMgICAgMSAgICAgIC0xLjI4 MiAtMTUuMjUxICAxMS4xOTIgIDEuMDAgIDAuMDAgICAgICBTT0xWDQpBVE9NICAgICAgMyAg SDEgIFRJUDMgICAgMSAgICAgIC0xLjMzMiAtMTYuMDUxICAxMC42NjkgIDEuMDAgIDAuMDAg ICAgICBTT0xWDQpBVE9NICAgICAgNCAgSDIgIFRJUDMgICAgMSAgICAgIC0wLjkyNiAtMTQu NTk1ICAxMC41OTIgIDEuMDAgIDAuMDAgICAgICBTT0xWDQoNCg0KKiogc2FtcGxlIGNvbnRh aW5pbmcgaW5mb3JtYXRpb24gYWJvdXQgdGhlIExKIHNvbHV0ZSBhbmQgb25lIG9mIHRoZSB3 YXRlciBtb2xlY3VsZXMgKiog ----50c0518d6b643cbb-- From owner-namd-l@rama.ks.uiuc.edu Mon Jan 5 10:40:30 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i05GeUtX002657 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Mon, 5 Jan 2004 10:40:30 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i05GeU97002656 for namd-l-outgoing; Mon, 5 Jan 2004 10:40:30 -0600 (CST) X-Authentication-Warning: rama.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 [130.126.120.65]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i05GeUtW002652 for ; Mon, 5 Jan 2004 10:40:30 -0600 (CST) Received: (from jim@localhost) by cancun.ks.uiuc.edu (8.9.3+Sun/8.9.1) id KAA09183 for namd-l@ks.uiuc.edu; Mon, 5 Jan 2004 10:40:30 -0600 (CST) Received: from poincare.ciril.fr (poincare.uhp-nancy.fr [194.214.217.19]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i05F2XtW028300 for ; Mon, 5 Jan 2004 09:02:34 -0600 (CST) Received: from dvorak (dvorak.edam.uhp-nancy.fr [194.214.125.170]) by poincare.ciril.fr (8.12.10/8.12.10/Guy-21-05-2003) with ESMTP id i05F28Jx009069 for ; Mon, 5 Jan 2004 16:02:08 +0100 (MET) From: =?iso-8859-1?q?J=E9r=F4me=20H=E9nin?= (by way of =?iso-8859-1?q?J=E9r=F4me=20H=E9nin?= ) Subject: Re: namd-l: alchemical free energy perturbation Date: Mon, 5 Jan 2004 16:10:52 +0100 User-Agent: KMail/1.5 To: namd-l@ks.uiuc.edu MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Message-Id: <200401051610.52649.jerome.henin@uhp-nancy.fr> X-Spam-Score: -100 () USER_IN_WHITELIST X-Scanned-By: poincare.ciril.fr Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by rama.ks.uiuc.edu id i05F2YtW028302 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, In your case, it will probably be easier to make the particle vanish than to make it appear, because when you simulate at lambda=0, the particle may overlap with water. To make it grow or shrink would require using the "single topology" method, wich is not supported by the FEP code in NAMD. However, there is no good reason why the dual-topology version should fail to describe your transformation. In your script, the following line : while {$step <= 1.00} { should be : while {$step < 1.00} { so that the last lambda window is [0.99, 1.0] and not [1.0, 1.01]. I checked the alchemical FEP tutorial : it contains the same error. I suppose you took it from there - sorry about that. I'm going to correct it as soon as possible. About the accuracy of your results, you should monitor the convergence of dG (the last column of the FEP output) in every window. 6400 fs is rather short, especially if half of it is not used for statistics. If the convergence is not reached, increase the sampling time (it may be wise to use larger times only for certain slow-converging windows). With a system as simple as yours, however, you shouldn't need a huge amount of sampling to obtain good results. Jerome > Hi, > I want to calculate the free energy change of growing a 3.0 ang. radius LJ > particle in water. I tried dual-topolgy method outlined in tutorial on NAMD > site but did not give expected free energy values. Is there any way to > 'grow/shrink' rather than going from lambda=0 (nothing) to lambda =1 (full > partcle)? Are they the same? I have also attached the config file, part of > the fep file (system.fep). The system is a LJ particle with 1000 water > molecules. thanks, > Amit. > PS: CMT is the atom type of the LJ particle that I have defined. -- Jérôme Hénin Equipe Dynamique des Assemblages Membranaires Université Henri Poincaré / CNRS UMR 7565 B.P. 239 54506 Vandoeuvre-lès-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@rama.ks.uiuc.edu Mon Jan 5 13:36:22 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i05JaMtX008298 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Mon, 5 Jan 2004 13:36:22 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i05JaMKA008297 for namd-l-outgoing; Mon, 5 Jan 2004 13:36:22 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from marcy.nas.nasa.gov (marcy.nas.nasa.gov [129.99.113.17]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i05JaLtW008292 for ; Mon, 5 Jan 2004 13:36:21 -0600 (CST) Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7p1+Sun/8.11.7/NAS-6n) with ESMTP id i05JaGr15095 for ; Mon, 5 Jan 2004 11:36:16 -0800 (PST) Date: Mon, 5 Jan 2004 11:36:16 -0800 (PST) From: Ioana Cozmuta To: namd-l@ks.uiuc.edu Subject: namd-l: SMD force (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi folks, I sent out this weekend an e-mail but perhaps got lost so I decided to forward it again. If anyone knows the right answer and could give me a hand I would appreciate that. Thanks a lot, Ioana ---------- Forwarded message ---------- Date: Sat, 3 Jan 2004 20:01:45 -0800 (PST) From: Ioana Cozmuta To: namd-l@ks.uiuc.edu Subject: SMD force Hi, Happy New Year to everybody and lots of successful simulations with NAMD in 2004! I have a short question related to SMD output. The manual says that at every SMD step the program writes out 1. the current timestep, 2. the current position of the center of mass of the restrained atoms and 3. the current force applied to the center of mass (pN). It is not clear to me what exactly does "current force applied to the center of mass" means: a. force due to dragging of the atoms with velocity v via a harmonical constraint k b. force due to the interaction with the surroundings c. both dragging force and interaction with the surroundings I want to use the information in the output to calculate only the component due to the interaction between the restrained atoms and the surroundings. Thanks in advance for your answer, Ioana From owner-namd-l@rama.ks.uiuc.edu Mon Jan 5 15:01:39 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i05L1ctX010773 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Mon, 5 Jan 2004 15:01:38 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i05L1cFh010772 for namd-l-outgoing; Mon, 5 Jan 2004 15:01:38 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from ku.edu.tr (ims.ku.edu.tr [193.140.63.3]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i05L1XtW010761 for ; Mon, 5 Jan 2004 15:01:35 -0600 (CST) Received: from ABAKAN [172.16.16.71] by ku.edu.tr with NIMS ModWeb Module; Mon, 05 Jan 2004 20:20:02 +0200 Subject: namd-l: Potential Terms From: AHMET BAKAN To: namd-l@ks.uiuc.edu Date: Mon, 05 Jan 2004 20:20:02 +0200 X-Mailer: NIMS ModWeb Module X-Sender: ABAKAN MIME-Version: 1.0 Message-ID: <1073326802.ce10bc80ABAKAN@KU.EDU.TR> Content-Type: multipart/mixed; boundary="------=_ModWebBOUNDARY_ce10bc80_1073326802" Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk This is a multi-part message in MIME format. --------=_ModWebBOUNDARY_ce10bc80_1073326802 Content-Type: text/plain; charset="ISO-8859-9" Content-Transfer-Encoding: quoted-printable Hi All, I have attached terms of a second generation force field potential calculat= ion. CHARMM includes some of those terms, so NAMD does. I do not know abo= ut architecture of NAMD, and wanna ask if it is simple to expand potentia= l terms of NAMD in order to use a second generation force field? It is pl= easure to have any comments, thanks. 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WMMq1rGStaxmPSta06rWtbK1rW59K1zjKte50rWudr0rXvOq173yta9+/etdCwAAOw== --------=_ModWebBOUNDARY_ce10bc80_1073326802-- From owner-namd-l@rama.ks.uiuc.edu Mon Jan 5 23:45:34 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i065jYtX027341 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Mon, 5 Jan 2004 23:45:34 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i065jYgP027340 for namd-l-outgoing; Mon, 5 Jan 2004 23:45:34 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from mail.ccnu.edu.cn ([202.114.32.3]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i065jPtW027336 for ; Mon, 5 Jan 2004 23:45:31 -0600 (CST) Received: (eyou send program); Tue, 06 Jan 2004 13:45:18 +0800 Message-ID: <273367918.10385@mail.ccnu.edu.cn> Received: from 202.114.34.252 by 202.114.32.3 with HTTP; Tue, 06 Jan 2004 13:45:18 +0800 X-WebMAIL-MUA: [202.114.34.252] From: "" To: namd-l@ks.uiuc.edu Date: Tue, 06 Jan 2004 13:45:18 +0800 Reply-To: "" Subject: namd-l: how to get "the rms force and maximum force" of energy minimization ? Content-Type: text/plain Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Dear sir, Whether has someone know how to get "the rms force and maximum force" of energy minimization in the output file with NAMD program? Whether are "INITIAL STEP and GRADIENT TOLERANCE" relevant to the above concept? Thank you for your information! From owner-namd-l@rama.ks.uiuc.edu Tue Jan 6 14:40:06 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i06Ke6tX019924 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Tue, 6 Jan 2004 14:40:06 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i06Ke6iL019923 for namd-l-outgoing; Tue, 6 Jan 2004 14:40:06 -0600 (CST) X-Authentication-Warning: rama.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 [130.126.120.65]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i06Ke5tW019919 for ; Tue, 6 Jan 2004 14:40:05 -0600 (CST) Received: (from jim@localhost) by cancun.ks.uiuc.edu (8.9.3+Sun/8.9.1) id OAA22217 for namd-l@ks.uiuc.edu; Tue, 6 Jan 2004 14:40:05 -0600 (CST) Received: from ux12.cso.uiuc.edu (root@ux12.cso.uiuc.edu [128.174.5.106]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i06JQmtW017443 for ; Tue, 6 Jan 2004 13:26:48 -0600 (CST) Received: from Zhilei (zhao4.scs.uiuc.edu [130.126.229.162]) by ux12.cso.uiuc.edu (8.12.10/8.12.10) with ESMTP id i06JQmxC020240 for ; Tue, 6 Jan 2004 13:26:48 -0600 (CST) From: "zhilei chen" To: Subject: namd-l: interaction energy Date: Tue, 6 Jan 2004 13:26:47 -0600 Message-ID: <000301c3d48b$06abf060$a2e57e82@Zhilei> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01C3D458.BC118060" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk This is a multi-part message in MIME format. ------=_NextPart_000_0004_01C3D458.BC118060 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear NAMD users, Sorry this might be a silly question;( I want to calculate the interaction energy between two residues. I used pairInteraction command in NAMD on the dcd file, and I got the VMD_FORCE and ELECT_FORCE, in the unit of kcal/mol/A. I am not sure how to convert this force into energy. Shall I just multiply the force by the distance between these two residues? Because each residues compose of multiple atoms, I don't know what distance I shall use. Thanks Zhilei ------=_NextPart_000_0004_01C3D458.BC118060 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Message
Dear = NAMD=20 users,
 
Sorry = this might be=20 a silly question;(
 
I want = to calculate=20 the interaction energy between two residues. I used pairInteraction = command in=20 NAMD on the dcd file, and I got the VMD_FORCE and ELECT_FORCE, in the = unit of=20 kcal/mol/A. I am not sure how to convert this force into energy. Shall I = just=20 multiply the force by the distance between these two residues? Because = each=20 residues compose of multiple atoms, I don't know what distance I = shall=20 use.
 
Thanks
 
Zhilei
------=_NextPart_000_0004_01C3D458.BC118060-- From owner-namd-l@rama.ks.uiuc.edu Tue Jan 6 17:15:00 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i06NExtX025235 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Tue, 6 Jan 2004 17:14:59 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i06NExRw025234 for namd-l-outgoing; Tue, 6 Jan 2004 17:14:59 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from ks.uiuc.edu (philo.ks.uiuc.edu [130.126.120.159]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i06NEutW025226; Tue, 6 Jan 2004 17:14:56 -0600 (CST) Message-ID: <3FFB4170.7695A7BA@ks.uiuc.edu> Date: Tue, 06 Jan 2004 17:14:56 -0600 From: Fangqiang Zhu X-Mailer: Mozilla 4.74 [en] (X11; U; SunOS 5.9 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: Ioana Cozmuta CC: namd-l@ks.uiuc.edu Subject: Re: namd-l: SMD force (fwd) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, > It is not clear to me what exactly does "current force applied to the > center of mass" means: > a. force due to dragging of the atoms with velocity v via a harmonical > constraint k > b. force due to the interaction with the surroundings > c. both dragging force and interaction with the surroundings The answer is a. > I want to use the information in the output to calculate only the > component due to the interaction between the restrained atoms and the > surroundings. Currently the only way to get the force on an atom arising from other atoms (in your word, the surroundings) in the simulation is to use the Tcl command "loadtotalforces". Please read the manual carefully for its usage. Zhu From owner-namd-l@rama.ks.uiuc.edu Tue Jan 6 18:25:28 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i070PStX027588 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Tue, 6 Jan 2004 18:25:28 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i070PSbC027587 for namd-l-outgoing; Tue, 6 Jan 2004 18:25:28 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from marcy.nas.nasa.gov (marcy.nas.nasa.gov [129.99.113.17]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i070PQtW027578; Tue, 6 Jan 2004 18:25:26 -0600 (CST) Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7p1+Sun/8.11.7/NAS-6n) with ESMTP id i070PKo13160; Tue, 6 Jan 2004 16:25:20 -0800 (PST) Date: Tue, 6 Jan 2004 16:25:20 -0800 (PST) From: Ioana Cozmuta To: Fangqiang Zhu cc: namd-l@ks.uiuc.edu Subject: Re: namd-l: SMD force (fwd) In-Reply-To: <3FFB4170.7695A7BA@ks.uiuc.edu> Message-ID: References: <3FFB4170.7695A7BA@ks.uiuc.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, Thank you for your reply. On Tue, 6 Jan 2004, Fangqiang Zhu wrote: > > It is not clear to me what exactly does "current force applied to the > > center of mass" means: > > a. force due to dragging of the atoms with velocity v via a harmonical > > constraint k > > b. force due to the interaction with the surroundings > > c. both dragging force and interaction with the surroundings > > The answer is a. > > > I want to use the information in the output to calculate only the > > component due to the interaction between the restrained atoms and the > > surroundings. > > Currently the only way to get the force on an atom arising from other > atoms (in your word, the surroundings) in the simulation is to use the Tcl > command "loadtotalforces". Please read the manual carefully for its > usage. > I have the information in SMD SMD time position (r_cm) force (F_drag) This means that I can calculate the interaction force two ways: 1. from Newton's EOM: F_interaction = m*a-F_drag (where a can be approximated from every three values of the r_cm in the SMD output) 2. From the pairInteraction module in NAMD as sum of vdw and electrostatic components F_interaction = F_vdw+F_electrostatic So in principle no matter if I use 1 or 2 I should get aprox the same value. Did anyone get to check this equality? Thanks, Ioana From owner-namd-l@rama.ks.uiuc.edu Tue Jan 6 22:14:23 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i074ENtX003453 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Tue, 6 Jan 2004 22:14:23 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i074ENcC003452 for namd-l-outgoing; Tue, 6 Jan 2004 22:14:23 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from jhuml4.jhu.edu (jhuml4.jhu.edu [128.220.2.67]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i074EMtW003448 for ; Tue, 6 Jan 2004 22:14:22 -0600 (CST) Received: from jhuml4.jhu.edu (jhuml4.jhu.edu [128.220.2.67]) by jhuml4.jhu.edu (PMDF V6.2-X17 #30840) with SMTP id <0HR300975QEGHC@jhuml4.jhu.edu> for namd-l@ks.uiuc.edu; Tue, 06 Jan 2004 23:14:21 -0500 (EST) Received: from jhuml4.jhu.edu ([128.220.2.67]) by jhuml4.jhu.edu (SAVSMTP 3.1.0.29) with SMTP id M2004010623142019575 for ; Tue, 06 Jan 2004 23:14:20 -0500 Received: from jhumail.jhu.edu (jhem1.jhmi.edu [162.129.8.22]) by jhuml4.jhu.edu (PMDF V6.2-X17 #30840) with ESMTP id <0HR300971QFXMY@jhuml4.jhu.edu> for namd-l@ks.uiuc.edu; Tue, 06 Jan 2004 23:14:21 -0500 (EST) Received: from [151.196.33.167] by jhumail.jhu.edu (mshttpd); Tue, 06 Jan 2004 23:20:10 -0500 Date: Tue, 06 Jan 2004 23:20:10 -0500 From: AMIT PALIWAL Subject: namd-l: total energy stuck between two levels To: namd-l@ks.uiuc.edu Message-id: <12179b1245c4.1245c412179b@jhumail.jhu.edu> MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.17 (built Jun 23 2003) Content-type: text/plain; charset=us-ascii Content-language: en Content-transfer-encoding: 7bit Content-disposition: inline X-Accept-Language: en Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi everyone, I have had this problem with the new namd version 2.5. Whenever I simulate peptide in water- first minimize the system and then start the production run- in the production run, the total energy oscillates beween two levels very far apart. I can not understand why?? Minimization seems to be perfectly fine. There was a suggestion to use separate thermostats for peptide and water. if this is the problem then how do you go about doing this? thanks, Amit. From owner-namd-l@rama.ks.uiuc.edu Wed Jan 7 02:33:38 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i078XctX009532 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 7 Jan 2004 02:33:38 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i078XbD1009531 for namd-l-outgoing; Wed, 7 Jan 2004 02:33:37 -0600 (CST) X-Authentication-Warning: rama.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 rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i078XatW009527 for ; Wed, 7 Jan 2004 02:33:37 -0600 (CST) Received: from dvorak (dvorak.edam.uhp-nancy.fr [194.214.125.170]) by poincare.ciril.fr (8.12.10/8.12.10/Guy-21-05-2003) with ESMTP id i078XXBa018147; Wed, 7 Jan 2004 09:33:33 +0100 (MET) From: =?iso-8859-1?q?J=E9r=F4me=20H=E9nin?= To: AMIT PALIWAL , namd-l@ks.uiuc.edu Subject: Re: namd-l: total energy stuck between two levels Date: Wed, 7 Jan 2004 09:42:33 +0100 User-Agent: KMail/1.5 References: <12179b1245c4.1245c412179b@jhumail.jhu.edu> In-Reply-To: <12179b1245c4.1245c412179b@jhumail.jhu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Message-Id: <200401070942.33046.jerome.henin@uhp-nancy.fr> X-Spam-Score: -100 () USER_IN_WHITELIST X-Scanned-By: poincare.ciril.fr Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by rama.ks.uiuc.edu id i078XbtW009528 Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi Amit, Are you using multiple timestepping? If yes, you should output energies with a period that is a multiple of the slowest timestep (normally fullElectFrequency). Otherwise, you may get incorrect energies. I don't think this is explained in the NAMD manual, but maybe it should. Jerome > Hi everyone, > I have had this problem with the new namd version 2.5. Whenever I simulate > peptide in water- first minimize the system and then start the production > run- in the production run, the total energy oscillates beween two levels > very far apart. I can not understand why?? Minimization seems to be > perfectly fine. There was a suggestion to use separate thermostats for > peptide and water. if this is the problem then how do you go about doing > this? thanks, > Amit. -- Jérôme Hénin Equipe Dynamique des Assemblages Membranaires Université Henri Poincaré / CNRS UMR 7565 B.P. 239 54506 Vandoeuvre-lès-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@rama.ks.uiuc.edu Wed Jan 7 09:22:29 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i07FMTtX018127 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 7 Jan 2004 09:22:29 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i07FMT4Z018126 for namd-l-outgoing; Wed, 7 Jan 2004 09:22:29 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from santiago.ks.uiuc.edu (santiago.ks.uiuc.edu [130.126.120.99]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i07FMRtW018122; Wed, 7 Jan 2004 09:22:27 -0600 (CST) Received: from localhost (jim@localhost) by santiago.ks.uiuc.edu (8.11.6/8.9.3) with ESMTP id i07FMRb31018; Wed, 7 Jan 2004 09:22:27 -0600 X-Authentication-Warning: santiago.ks.uiuc.edu: jim owned process doing -bs Date: Wed, 7 Jan 2004 09:22:27 -0600 (CST) From: Jim Phillips To: AMIT PALIWAL cc: namd-l@ks.uiuc.edu Subject: Re: namd-l: total energy stuck between two levels In-Reply-To: <12179b1245c4.1245c412179b@jhumail.jhu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, I suspect that your outputEnergies period (e.g., 10) is not a multiple of your fullElectFrequency period (e.g., 4). The logic that avoids the extra math to calculate ELECT energies that the user never sees doesn't anticipate this, so half of the energy output are missing the long-range ELECT energy component. The other energy terms should be OK. Minimization uses energies directly and therefore always calculates them. -Jim On Tue, 6 Jan 2004, AMIT PALIWAL wrote: > Hi everyone, I have had this problem with the new namd version 2.5. > Whenever I simulate peptide in water- first minimize the system and then > start the production run- in the production run, the total energy > oscillates beween two levels very far apart. I can not understand why?? > Minimization seems to be perfectly fine. There was a suggestion to use > separate thermostats for peptide and water. if this is the problem then > how do you go about doing this? thanks, Amit. > From owner-namd-l@rama.ks.uiuc.edu Wed Jan 7 09:45:21 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i07FjLtX018894 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 7 Jan 2004 09:45:21 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i07FjLc0018893 for namd-l-outgoing; Wed, 7 Jan 2004 09:45:21 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from santiago.ks.uiuc.edu (santiago.ks.uiuc.edu [130.126.120.99]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i07FjBtW018888; Wed, 7 Jan 2004 09:45:11 -0600 (CST) Received: from localhost (jim@localhost) by santiago.ks.uiuc.edu (8.11.6/8.9.3) with ESMTP id i07FjBt31106; Wed, 7 Jan 2004 09:45:11 -0600 X-Authentication-Warning: santiago.ks.uiuc.edu: jim owned process doing -bs Date: Wed, 7 Jan 2004 09:45:11 -0600 (CST) From: Jim Phillips To: AHMET BAKAN cc: namd-l@ks.uiuc.edu Subject: Re: namd-l: Potential Terms In-Reply-To: <1073326802.ce10bc80ABAKAN@KU.EDU.TR> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi, It wouldn't be simple, but most of the complication would come from managing the parameters. I assume that the cross terms (e.g., angle-angle-dihedral) are all local (i.e., part of the same dihedral). I'll keep this in mind in the design of future versions. Thanks. -Jim On Mon, 5 Jan 2004, AHMET BAKAN wrote: > Hi All, I have attached terms of a second generation force field > potential calculation. CHARMM includes some of those terms, so NAMD > does. I do not know about architecture of NAMD, and wanna ask if it is > simple to expand potential terms of NAMD in order to use a second > generation force field? It is pleasure to have any comments, thanks. > Ahmet ==============ABC============== Ahmet BAKAN Chemistry, Junior Koc > University abakan@ku.edu.tr ICQ #86167698 http://home.ku.edu.tr/~abakan > From owner-namd-l@rama.ks.uiuc.edu Wed Jan 7 10:12:23 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i07GCNtX019786 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 7 Jan 2004 10:12:23 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i07GCNnw019785 for namd-l-outgoing; Wed, 7 Jan 2004 10:12:23 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from jhuml4.jhu.edu (jhuml4.jhu.edu [128.220.2.67]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i07GCNtW019781 for ; Wed, 7 Jan 2004 10:12:23 -0600 (CST) Received: from jhuml4.jhu.edu (jhuml4.jhu.edu [128.220.2.67]) by jhuml4.jhu.edu (PMDF V6.2-X17 #30840) with SMTP id <0HR40013HNLNCG@jhuml4.jhu.edu> for namd-l@ks.uiuc.edu; Wed, 07 Jan 2004 11:12:22 -0500 (EST) Received: from jhuml4.jhu.edu ([128.220.2.67]) by jhuml4.jhu.edu (SAVSMTP 3.1.0.29) with SMTP id M2004010711122107425 for ; Wed, 07 Jan 2004 11:12:21 -0500 Received: from jhu.edu (shiva.che.jhu.edu [128.220.103.172]) by jhuml4.jhu.edu (PMDF V6.2-X17 #30840) with ESMTP id <0HR4001E4NOLCG@jhuml4.jhu.edu> for namd-l@ks.uiuc.edu; Wed, 07 Jan 2004 11:12:21 -0500 (EST) Date: Wed, 07 Jan 2004 06:10:03 -0500 From: Amit Paliwal Subject: [Fwd: namd-l: total energy stuck between two levels] To: namd-l@ks.uiuc.edu Message-id: <3FFBE90B.A57503B7@jhu.edu> Organization: Chemical Engineering Department MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-3 i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk > Thanks Jim and Jerome, > That was indeed the case ...I will take that into account. > -Amit. > > Jim Phillips wrote: > > > Hi, > > > > I suspect that your outputEnergies period (e.g., 10) is not a multiple of > > your fullElectFrequency period (e.g., 4). The logic that avoids the extra > > math to calculate ELECT energies that the user never sees doesn't > > anticipate this, so half of the energy output are missing the long-range > > ELECT energy component. The other energy terms should be OK. > > > > Minimization uses energies directly and therefore always calculates them. > > > > -Jim > > > > On Tue, 6 Jan 2004, AMIT PALIWAL wrote: > > > > > Hi everyone, I have had this problem with the new namd version 2.5. > > > Whenever I simulate peptide in water- first minimize the system and then > > > start the production run- in the production run, the total energy > > > oscillates beween two levels very far apart. I can not understand why?? > > > Minimization seems to be perfectly fine. There was a suggestion to use > > > separate thermostats for peptide and water. if this is the problem then > > > how do you go about doing this? thanks, Amit. > > > From owner-namd-l@rama.ks.uiuc.edu Wed Jan 7 13:05:35 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i07J5ZtX025628 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 7 Jan 2004 13:05:35 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i07J5ZDw025627 for namd-l-outgoing; Wed, 7 Jan 2004 13:05:35 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from jhuml3.jhu.edu (jhuml3.jhu.edu [128.220.2.66]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i07J5YtW025623 for ; Wed, 7 Jan 2004 13:05:34 -0600 (CST) Received: from jhuml3.jhu.edu (jhuml3.jhu.edu [128.220.2.66]) by jhuml3.jhu.edu (PMDF V6.2-X17 #30840) with SMTP id <0HR400ERIVKG7R@jhuml3.jhu.edu> for namd-l@ks.uiuc.edu; Wed, 07 Jan 2004 14:05:32 -0500 (EST) Received: from jhuml3.jhu.edu ([128.220.2.66]) by jhuml3.jhu.edu (SAVSMTP 3.1.0.29) with SMTP id M2004010714053210173 for ; Wed, 07 Jan 2004 14:05:32 -0500 Received: from jhu.edu (shiva.che.jhu.edu [128.220.103.172]) by jhuml3.jhu.edu (PMDF V6.2-X17 #30840) id <0HR400F01VP8TN@jhuml3.jhu.edu> (original mail from paliwal@jhu.edu) for namd-l@ks.uiuc.edu; Wed, 07 Jan 2004 14:05:32 -0500 (EST) Received: from jhu.edu (shiva.che.jhu.edu [128.220.103.172]) by jhuml3.jhu.edu (PMDF V6.2-X17 #30840) with ESMTP id <0HR400CZ7VP75J@jhuml3.jhu.edu> for namd-l@ks.uiuc.edu; Wed, 07 Jan 2004 14:05:31 -0500 (EST) Date: Wed, 07 Jan 2004 09:03:12 -0500 From: Amit Paliwal Subject: namd-l: Interaction energy between fixed atoms To: Jim Phillips Cc: namd-l@ks.uiuc.edu Message-id: <3FFC11A0.FE707F2A@jhu.edu> Organization: Chemical Engineering Department MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-3 i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi All, Just had a small question: How does NAMD handle fixed atoms , lets say in constant pressure simulation? Do the energy values include the interaction energy between the pairs of fixed atoms? Also when 'fixedatomsforces' option is on then does it do more than just displaying the current forces acting on these atoms? Sorry if this is too simple a question but did not quite get it from the userguide. thanks, Amit. From owner-namd-l@rama.ks.uiuc.edu Thu Jan 8 02:40:11 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i088eBtX016225 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Thu, 8 Jan 2004 02:40:11 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i088eBgS016224 for namd-l-outgoing; Thu, 8 Jan 2004 02:40:11 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from safe17.bezeqint.net (safe17.bezeqint.net [212.179.95.63]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i088eAtW016220 for ; Thu, 8 Jan 2004 02:40:10 -0600 (CST) Received: from safe17.bezeqint.net (localhost [127.0.0.1]) by safe17.bezeqint.net (Bezeq International SMTP out Mail Server) with SMTP id 532CA2080BF for ; Thu, 8 Jan 2004 10:40:08 +0200 (IST) Received: from bela.bezeqint.net ([IP=192.115.104.7]) by eSafe SMTP Relay 1073546425; Thu Jan 8 10:40:07 2004 Received: from mail.proteologics.com (bzq-179-34-98.cust.bezeqint.net [212.179.34.98]) by bela.bezeqint.net (Bezeq International SMTP out Mail Server) with ESMTP id EE64A33E7B for ; Thu, 8 Jan 2004 10:34:06 +0200 (IST) Received: from [10.0.0.100] (IDENT:20f7502e2d319f216529e9dc4d4f8c8d@pooh.proteologics.com [10.0.0.100]) by mail.proteologics.com (8.11.6/8.11.6) with ESMTP id i088e6e27296 for ; Thu, 8 Jan 2004 10:40:06 +0200 Subject: Re: namd-l: Charm++ nodelist commands From: Gadi Oron To: namd-l@ks.uiuc.edu In-Reply-To: References: Content-Type: text/plain Organization: Proteologics Message-Id: <1073551206.10405.27.camel@pooh.proteologics.com> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.5 (1.4.5-7) Date: Thu, 08 Jan 2004 10:40:06 +0200 Content-Transfer-Encoding: 7bit Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Hi again, Sorry for the late reply, but I was sick for a couple of days. On Wed, 2003-12-31 at 19:59, Gengbin Zheng wrote: > > > Please find the NAMD binary compiled with Windows VC++ 6.0 at: > > > http://www.ks.uiuc.edu/~gzheng/NAMD_Win32-i686.zip Ok, I've used your Win32 version along with a recompiled linux version and everything is working just great! So, on to the next step (distributing NAMD over the entire network and running charmd as service). Many thanks. -- ================= Gadi ORON, PhD -o- Proteologics ====================== ========== gadi/at/proteologics.com ========== +972 8 9475666 ========== Some men rob you with a six-gun -- others with a fountain pen. -- Woodie Guthrie From owner-namd-l@rama.ks.uiuc.edu Fri Jan 9 16:45:32 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i09MjWtX019056 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 9 Jan 2004 16:45:32 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i09MjWkr019055 for namd-l-outgoing; Fri, 9 Jan 2004 16:45:32 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from batch3.csd.uwm.edu (batch3.csd.uwm.edu [129.89.169.226]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i09MjVtW019051 for ; Fri, 9 Jan 2004 16:45:31 -0600 (CST) Received: from mail06.imt.uwm.edu (mail06.imt.uwm.edu [129.89.7.48]) by batch3.csd.uwm.edu (8.12.10/8.12.6) with ESMTP id i09MjV1Z024898 for ; Fri, 9 Jan 2004 16:45:31 -0600 (CST) Received: from mail06.imt.uwm.edu (localhost [127.0.0.1]) by mail06.imt.uwm.edu (8.12.10/8.12.5) with ESMTP id i09MjVVk004635 for ; Fri, 9 Jan 2004 16:45:31 -0600 Received: (from wwwrun@localhost) by mail06.imt.uwm.edu (8.12.10/8.12.6/Submit) id i09MjVJZ004634 for namd-l@ks.uiuc.edu; Fri, 9 Jan 2004 16:45:31 -0600 Received: from watson.math.uwm.edu (watson.math.uwm.edu [129.89.14.144]) by mail06.imt.uwm.edu (IMP) with HTTP for ; Fri, 9 Jan 2004 16:45:30 -0600 Message-ID: <1073688330.3fff2f0b03a37@mail06.imt.uwm.edu> Date: Fri, 9 Jan 2004 16:45:31 -0600 From: junxie@uwm.edu To: "namd-l@ks.uiuc.edu" Subject: namd-l: limit on the number of residues in each segment 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 X-Originating-IP: 129.89.14.144 X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=-48.217 required=5 tests=NO_REAL_NAME,TO_ADDRESS_EQ_REAL,UWM_DOMAIN_MESSAGE_0 X-Scanned-By: MIMEDefang 2.31 (www . roaringpenguin . com / mimedefang) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk Is there any limit on the number of residues in each segment, when using "psfgen" to generate a psf file? Thanks. From owner-namd-l@rama.ks.uiuc.edu Fri Jan 9 16:41:52 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i09MfqtX018959 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 9 Jan 2004 16:41:52 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i09MfqL1018958 for namd-l-outgoing; Fri, 9 Jan 2004 16:41:52 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from batch3.csd.uwm.edu (batch3.csd.uwm.edu [129.89.169.226]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i09MfptW018954 for ; Fri, 9 Jan 2004 16:41:52 -0600 (CST) Received: from mail06.imt.uwm.edu (mail06.imt.uwm.edu [129.89.7.48]) by batch3.csd.uwm.edu (8.12.10/8.12.6) with ESMTP id i09Mfp1Z031091 for ; Fri, 9 Jan 2004 16:41:51 -0600 (CST) Received: from mail06.imt.uwm.edu (localhost [127.0.0.1]) by mail06.imt.uwm.edu (8.12.10/8.12.5) with ESMTP id i09MfpVk003368 for ; Fri, 9 Jan 2004 16:41:51 -0600 Received: (from wwwrun@localhost) by mail06.imt.uwm.edu (8.12.10/8.12.6/Submit) id i09Mfppm003367 for namd-l@ks.uiuc.edu; Fri, 9 Jan 2004 16:41:51 -0600 Received: from watson.math.uwm.edu (watson.math.uwm.edu [129.89.14.144]) by mail06.imt.uwm.edu (IMP) with HTTP for ; Fri, 9 Jan 2004 16:41:51 -0600 Message-ID: <1073688111.3fff2e2f5f318@mail06.imt.uwm.edu> Date: Fri, 9 Jan 2004 16:41:51 -0600 From: junxie@uwm.edu To: namd-l@ks.uiuc.edu Subject: namd-l: RATTLE Alg 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 X-Originating-IP: 129.89.14.144 X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=-48.661 required=5 tests=NO_REAL_NAME,UWM_DOMAIN_MESSAGE_0 X-Scanned-By: MIMEDefang 2.31 (www . roaringpenguin . com / mimedefang) Sender: owner-namd-l@ks.uiuc.edu Precedence: bulk I know we can apply RATTLE algorithm to bonds between hydrogen and its mother atom in a hydrogen group. But can we apply this algorithm to any bond in the system, eg. the backbone bonds ? Thanks. From owner-namd-l@rama.ks.uiuc.edu Fri Jan 9 16:53:27 2004 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i09MrRtX019379 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 9 Jan 2004 16:53:27 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id i09MrRWq019378 for namd-l-outgoing; Fri, 9 Jan 2004 16:53:27 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f Received: from youkai.llnl.gov (youkai.llnl.gov [134.9.187.176]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i09MrQtX019368 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 9 Jan 2004 16:53:26 -0600 (CST) Received: from youkai.llnl.gov (youkai.llnl.gov [134.9.187.176]) by youkai.llnl.gov (8.12.10/8.12.10) with ESMTP id i09MrKOZ000973; Fri, 9 Jan 2004 14:53:20 -0800 Date: Fri, 9 Jan 2004 14:53:20 -0800 (PST) From: Brian Bennion