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From: bioinfo Gu <bioinfowistar@yahoo.com>
Subject: build NAMD
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Hello, 
 
I am try to build NAMD from source code. 
 
Source version: NAMD_2.5b1_Source
charm-5.4
arch : Linux-ia64
 
when I compile, it gives me some error:
 
 ecpc -D_IA64 -I/usr/local/gnu/include -DSOCKLEN_T=socklen_t -I/usr/compbio/NAMD_2.5b1_Source/charm-5.4/include -Isrc -Iinc   -I/usr/compbio/tcl8.3/include -I/root/tcl-linux/include -DNAMD_TCL -I/usr/compbio/fftw-3.0.1/include -I/root/fftw-linux/include -DNAMD_FFTW  -O2 -DCMK_OPTIMIZE -DNAMD_VERSION=\"2.5b1\" -DNAMD_PLATFORM=\"Linux-ia64\"    -o obj/ComputeHomePatches.o -c src/ComputeHomePatches.C
/usr/compbio/NAMD_2.5b1_Source/charm-5.4/include/charm++.h(70): warning #873: function "Chare::operator new(size_t={_Sizet={unsigned long}}, void *)" has no corresponding operator delete (to be called if an exception is thrown during initialization of an allocated object)
      void *operator new(size_t, void *ptr) { return ptr; };
            ^
src/UniqueSortedArray.h(59): error: no suitable conversion function from "const PatchElem" to "const void *" exists
    this->found = bsearch(elem);
                          ^
          detected during:
            instantiation of "int UniqueSortedArray<Elem>::insert(const Elem &) [with Elem=PatchElem]" at line 50
            instantiation of "int UniqueSortedArray<Elem>::add(const Elem &) [with Elem=PatchElem]" 
src/UniqueSortedArray.h(59): error #165: too few arguments in function call
    this->found = bsearch(elem);
                              ^
          detected during:
            instantiation of "int UniqueSortedArray<Elem>::insert(const Elem &) [with Elem=PatchElem]" at line 50
            instantiation of "int UniqueSortedArray<Elem>::add(const Elem &) [with Elem=PatchElem]" 
src/UniqueSortedArray.h(59): warning #556: a value of type "void *" cannot be assigned to an entity of type "int"
    this->found = bsearch(elem);
                ^
          detected during:
            instantiation of "int UniqueSortedArray<Elem>::insert(const Elem &) [with Elem=PatchElem]" at line 50
            instantiation of "int UniqueSortedArray<Elem>::add(const Elem &) [with Elem=PatchElem]" 
compilation aborted for src/ComputeHomePatches.C (code 2)
make: *** [obj/ComputeHomePatches.o] Error 2

 
Thanks a lot,
 
Grace


---------------------------------
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<DIV>Hello, </DIV>
<DIV>&nbsp;</DIV>
<DIV>I am try to build NAMD from source code. </DIV>
<DIV>&nbsp;</DIV>
<DIV>Source version: NAMD_2.5b1_Source</DIV>
<DIV>charm-5.4</DIV>
<DIV>arch : Linux-ia64</DIV>
<DIV>&nbsp;</DIV>
<DIV>when I&nbsp;compile,&nbsp;it gives&nbsp;me some error:</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;ecpc -D_IA64 -I/usr/local/gnu/include -DSOCKLEN_T=socklen_t -I/usr/compbio/NAMD_2.5b1_Source/charm-5.4/include -Isrc -Iinc&nbsp;&nbsp; -I/usr/compbio/tcl8.3/include -I/root/tcl-linux/include -DNAMD_TCL -I/usr/compbio/fftw-3.0.1/include -I/root/fftw-linux/include -DNAMD_FFTW&nbsp; -O2 -DCMK_OPTIMIZE -DNAMD_VERSION=\"2.5b1\" -DNAMD_PLATFORM=\"Linux-ia64\"&nbsp;&nbsp;&nbsp; -o obj/ComputeHomePatches.o -c src/ComputeHomePatches.C<BR>/usr/compbio/NAMD_2.5b1_Source/charm-5.4/include/charm++.h(70): warning #873: function "Chare::operator new(size_t={_Sizet={unsigned long}}, void *)" has no corresponding operator delete (to be called if an exception is thrown during initialization of an allocated object)<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; void *operator new(size_t, void *ptr) { return ptr; };<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ^</DIV>
<DIV>src/UniqueSortedArray.h(59): error: no suitable conversion function from "const PatchElem" to "const void *" exists<BR>&nbsp;&nbsp;&nbsp; this-&gt;found = bsearch(elem);<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ^<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; detected during:<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; instantiation of "int UniqueSortedArray&lt;Elem&gt;::insert(const Elem &amp;) [with Elem=PatchElem]" at line 50<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; instantiation of "int UniqueSortedArray&lt;Elem&gt;::add(const Elem &amp;) [with Elem=PatchElem]" </DIV>
<DIV>src/UniqueSortedArray.h(59): error #165: too few arguments in function call<BR>&nbsp;&nbsp;&nbsp; this-&gt;found = bsearch(elem);<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ^<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; detected during:<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; instantiation of "int UniqueSortedArray&lt;Elem&gt;::insert(const Elem &amp;) [with Elem=PatchElem]" at line 50<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; instantiation of "int UniqueSortedArray&lt;Elem&gt;::add(const Elem &amp;) [with Elem=PatchElem]" </DIV>
<DIV>src/UniqueSortedArray.h(59): warning #556: a value of type "void *" cannot be assigned to an entity of type "int"<BR>&nbsp;&nbsp;&nbsp; this-&gt;found = bsearch(elem);<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ^<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; detected during:<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; instantiation of "int UniqueSortedArray&lt;Elem&gt;::insert(const Elem &amp;) [with Elem=PatchElem]" at line 50<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; instantiation of "int UniqueSortedArray&lt;Elem&gt;::add(const Elem &amp;) [with Elem=PatchElem]" </DIV>
<DIV>compilation aborted for src/ComputeHomePatches.C (code 2)<BR>make: *** [obj/ComputeHomePatches.o] Error 2<BR></DIV>
<DIV>&nbsp;</DIV>
<DIV>Thanks&nbsp;a lot,</DIV>
<DIV>&nbsp;</DIV>
<DIV>Grace</DIV><p><hr SIZE=1>
Do you Yahoo!?<br>
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From owner-namd-l@rama.ks.uiuc.edu Thu Sep 11 22:42:20 2003
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Subject: libc6 on debian x86
From: "Grischa R. Meyer" <grischa@graduates.uwa.edu.au>
To: namd-l@ks.uiuc.edu
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Hi,

I updated libc on our debian (sid) systems to version 2.3.2-6 and namd
doesn't run anymore, there are problems with libnss_compat, which was
changed in this version.

I was wondering if there will be binaries available that work with the
new library, or if I need to compile my own.

The error was as follows:
$ charmrun ++local /opt/bin/namd2.5b2
Info: NAMD 2.5b2 for Linux-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd@ks.uiuc.edu
Info:
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Built Wed Jun 11 22:12:20 CDT 2003 by justin on
aberdeen.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP.
------------- Processor 0 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory
paranoid'.
Stack Traceback:
  [0] [0x82c1348]
  [1] /lib/libc.so.6 [0x40143dce]
  [2] /lib/libc.so.6 [0x40143ee8]
  [3] __nss_lookup_function+0x1f9  [0x40123399]
  [4] /lib/libnss_compat.so.2 [0x4002136e]
  [5] _nss_compat_getpwuid_r+0xc5  [0x40022f05]
  [6] [0x82e3129]
  [7] [0x82e2cd7]
  [8] [0x804a2f7]
  [9] [0x804d590]
Fatal error on PE 0> segmentation violation

Thanks,

Grischa


-- 
Grischa R. Meyer, grischa@graduates.uwa.edu.au



From owner-namd-l@rama.ks.uiuc.edu Mon Sep 15 19:51:51 2003
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Date: Mon, 15 Sep 2003 19:51:49 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: namd-l@ks.uiuc.edu
Subject: NAMD 2.5b2 Released
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Dear NAMD Users,

At long last, the winds of change have blown as one and NAMD 2.5b2 is
ready for general use.  This should be very close to version 2.5 final, so
please try it out and let namd@ks.uiuc.edu know of any stability or other
problems.  Be sure to check the release notes, and also look for many new
tutorials and and the experimental NAMD Wiki on the main NAMD page at
http://www.ks.uiuc.edu/Research/namd/

-Jim


+--------------------------------------------------------------------+
|                                                                    |
|                  NAMD 2.5b2 Release Announcement                   |
|                                                                    |
+--------------------------------------------------------------------+

                                                  September 15, 2003

The Theoretical and Computational Biophysics Group at the University of
Illinois is proud to announce the public release of a new version of
NAMD, a parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems.  NAMD is
distributed free of charge and includes source code.  NAMD development
is supported by the NIH National Center for Research Resources.

NAMD 2.5b2 has several advantages over NAMD 2.4:

- Improved parallel scaling and serial performance.

- Trajectory reading and interaction energy analysis.

- Improved constant pressure simulation and coordinate wrapping.

NAMD is available from http://www.ks.uiuc.edu/Research/namd/.

For your convenience, NAMD has been ported to and will be installed
on the machines at the NSF-sponsored national supercomputing centers.
If you are planning substantial simulation work of an academic nature
you should apply for these resources.  Benchmarks for your proposal
are available at http://www.ks.uiuc.edu/Research/namd/performance.html

The Theoretical and Computational Biophysics Group encourages NAMD users
to be closely involved in the development process through reporting
bugs, contributing fixes, periodical surveys and via other means.
Questions or comments may be directed to namd@ks.uiuc.edu.

We are eager to hear from you, and thank you for using our software!



From owner-namd-l@rama.ks.uiuc.edu Mon Sep 15 23:45:35 2003
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Date: Mon, 15 Sep 2003 21:43:52 -0700 (PDT)
From: Brian Bennion <brian@youkai.llnl.gov>
To: namd-l@ks.uiuc.edu
Subject: Thank you 
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Thank you NAMD developers!!!

I know many have waited for the creation of this list.  I am also glad to 
see that my puny suggestion of an index to the namd manual was 
implemented.

Thanks again
Brian

 -- 
*****************************************************************
**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1@llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **
*****************************************************************



From owner-namd-l@rama.ks.uiuc.edu Tue Sep 16 14:12:49 2003
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From: "Cheri M Turman" <Cheri.M.Turman@uth.tmc.edu>
To: namd-l@ks.uiuc.edu
Message-ID: <95033cf2.3cf29503@uth.tmc.edu>
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Hi, 
I have been successfully running NAMD on many cytochrome p450s for
awhile now and for some reason I am getting a segmentation fault on only
 one of the isoforms.  The only differences between the runs can only be
in the psf and pdb files because the .config are the same for all
proteins I run.  I also used the same psfgen utility within NAMD to
create the psf files so that should not be the problem.  The only major
difference I can see is the cell origin.  My other successful protein's
origins were only + integers and with this problem potein, they are all
-.  Seg faults usually deal with stacksize so I am thinking, does the
cell origin (-7 -19 -30) cause the program to require more memory?  Can
anyone comment on this and help me out?  Also, does anyone know how I
might recenter the protein and try my hypothesis.  I am trying in VMD
but I haven't got that to work just yet.  I am attaching the .log just
in case.
Cheers,
Cheri   




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030

    e-mail: cheri.m.turman@uth.tmc.edu
    Ph.: 713-500-6126
    Fax: 713-500-0652

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From owner-namd-l@rama.ks.uiuc.edu Tue Sep 16 15:27:12 2003
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Date: Tue, 16 Sep 2003 15:27:10 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: Cheri M Turman <Cheri.M.Turman@uth.tmc.edu>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: segmentation fault
In-Reply-To: <95033cf2.3cf29503@uth.tmc.edu>
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Cheri,

I see this error message in your log file:

  Warning: Not all atoms have unique coordinates.

What this really means is that two atoms were unphysically close together
and were treated as being excluded.  The likely interpretation is that the
atoms have the same coordinates, probably because they are actually
uninitialized and were set to the default value (0,0,0) by psfgen.

Of course, a segmentation fault shouldn't happen under any circumstance.
Please see if the problem also happens with the just-released 2.5b2.

-Jim


On Tue, 16 Sep 2003, Cheri M Turman wrote:

> Hi,
> I have been successfully running NAMD on many cytochrome p450s for
> awhile now and for some reason I am getting a segmentation fault on only
>  one of the isoforms.  The only differences between the runs can only be
> in the psf and pdb files because the .config are the same for all
> proteins I run.  I also used the same psfgen utility within NAMD to
> create the psf files so that should not be the problem.  The only major
> difference I can see is the cell origin.  My other successful protein's
> origins were only + integers and with this problem potein, they are all
> -.  Seg faults usually deal with stacksize so I am thinking, does the
> cell origin (-7 -19 -30) cause the program to require more memory?  Can
> anyone comment on this and help me out?  Also, does anyone know how I
> might recenter the protein and try my hypothesis.  I am trying in VMD
> but I haven't got that to work just yet.  I am attaching the .log just
> in case.
> Cheers,
> Cheri
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Cheri M. Turman
>    Graduate Student
>    University of Texas-Houston Medical School
>     6431 Fannin
>     Houston, TX 77030
>
>     e-mail: cheri.m.turman@uth.tmc.edu
>     Ph.: 713-500-6126
>     Fax: 713-500-0652
>



From owner-namd-l@rama.ks.uiuc.edu Tue Sep 16 16:24:29 2003
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Date: Tue, 16 Sep 2003 14:22:44 -0700 (PDT)
From: Brian Bennion <brian@youkai.llnl.gov>
To: Cheri M Turman <Cheri.M.Turman@uth.tmc.edu>
cc: namd-l@ks.uiuc.edu
Subject: namd-l: Re: seg fault
In-Reply-To: <9be5ba61.ba619be5@uth.tmc.edu>
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Hi Cheri,

Jim is right, after looking at your logfile and seeing the energies, no 
wonder namd is choking...

Warning: Not all atoms have unique coordinates.
ETITLE:     TS    BOND        ANGLE       DIHED       IMPRP       ELECT       
VDW       BOUNDARY    MISC        KINETIC
       TOTAL     TEMP     PRESSURE    GPRESSURE    VOLUME     PRESSAVG    
GPRESSAVG
ENERGY:      0 13373540.4319 99999999.9999 1986.8588   99999999.9999 
-111162.1731 5796362.1421 0.0000      0.0000      0
.0000      99999999.9999 0.0000      99999999.9999 99999999.9999 
429831.6119 99999999.9999 99999999.9999
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
SEGMENTATION FAULT

The sun doesn't get this hot!

There are to atoms bonded together in the psf file that are on top of each 
other in coordinate space.

Looking at your pdbfile I see that all the heme hydrogen atoms have no 
coordinates, they are all sitting at 0 0 0

I thought Heme wasn't in here?

Brian



-- 
*****************************************************************
**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1@llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **
*****************************************************************



From owner-namd-l@rama.ks.uiuc.edu Tue Sep 16 17:57:10 2003
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Date: Tue, 16 Sep 2003 18:06:20 +0000
From: Jerry Ebalunode <jebalunode@UH.EDU>
Subject: namd-l: error in notes on compiling namd2.5b2 with plugins
To: namd-l@ks.uiuc.edu
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Hi all,
It seems you don't  have to edit  the  arch/ARCH.plugins file to fix the 
library and header path but you should rather edit the arch/All-Unix.plugins 
file to set the path.
-- 
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


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Date: Tue, 16 Sep 2003 18:44:49 +0000
From: Jerry Ebalunode <jebalunode@UH.EDU>
Subject: namd-l: output warning in using namd2
 "Warning: Not all atoms have unique coordinates."
To: namd-l@ks.uiuc.edu
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Hi all,
I just compiled namd2.5b2  on an itanium2 cluster that uses SCALI's 
implementation of the mpi. When I run the binary, I always get this warning
"Warning: Not all atoms have unique coordinates." in the output log.  Does 
anyone know how to correct this problem? I initially thought it had to do 
with the tcl or fftw libraries I was using,  so used the precompiled 
libraries from http://www.ks.uiuc.edu/Research/namd/libraries/ meant for my 
architecture. However, after recompiling and running namd2  I still had the 
same problems. 


Compiler information
intel C/C++ compiler  for itanium ecc version 7.1

-- 
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 Tue Sep 16 21:19:05 2003
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Date: Tue, 16 Sep 2003 21:19:03 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: Jerry Ebalunode <jebalunode@UH.EDU>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: output warning in using namd2 "Warning: Not all atoms
 have unique coordinates."
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This error happens on every test simulation, and they used to work?  Hmmm.
Your compiler and processor are both newer that what I've gotten to test
at NCSA, and the "unique coordinates" warning really means that extra
exclusions were calculated, which is very unusual.  You might want to back
off on the optimization of ComputeNonbonded..., maybe start by commenting
out CXXNOALIASOPTS from arch/Linux-ia64-ecc.arch.  If that eliminates the
warning then we're at least on the right track (but Itanium is pretty
pointless without those optimization flags).

-Jim


On Tue, 16 Sep 2003, Jerry Ebalunode wrote:

> Hi all,
> I just compiled namd2.5b2  on an itanium2 cluster that uses SCALI's
> implementation of the mpi. When I run the binary, I always get this warning
> "Warning: Not all atoms have unique coordinates." in the output log.  Does
> anyone know how to correct this problem? I initially thought it had to do
> with the tcl or fftw libraries I was using,  so used the precompiled
> libraries from http://www.ks.uiuc.edu/Research/namd/libraries/ meant for my
> architecture. However, after recompiling and running namd2  I still had the
> same problems.
>
>
> Compiler information
> intel C/C++ compiler  for itanium ecc version 7.1
>
> --
> 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 Wed Sep 17 10:43:52 2003
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Date: Wed, 17 Sep 2003 05:36:51 +0100 (BST)
From: =?iso-8859-1?q?srinivasa=20murthy?= <srim729@yahoo.co.in>
Subject: namd-l: help needed on node list
To: namd-l@ks.uiuc.edu
Cc: gsmurthy@imsc.res.in
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hi,
   We are running the new version of namd(non MPI
version) on our cluster(9 nodes dual cpus with
multithreading). When we try to launch job on say 18
processors, though the each node takes two jobs and
job
is completed successfully, the wall time will be twice
(or more) than that of cpu time.Suppose if we had used
only 4 nodes and launched job on 8 processors, the
time
taken to complete the job will be twice that of what
we
would have got if we had launched the job on 8
nodes(now each node taking only one job). I tried to
change my node list file my including each host 4
times..but this did not work. The new user's guide had
solution for this kind of problem provided there was
pre-existing queueing system.. But our cluster has no
queueing system.

How can we use the cluster upto its full 'potential'..

regards
srinivasa



________________________________________________________________________
Yahoo! India Matrimony: Find your partner online.
Go to http://yahoo.shaadi.com

From owner-namd-l@rama.ks.uiuc.edu Wed Sep 17 11:12:42 2003
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Date: Wed, 17 Sep 2003 11:21:53 +0000
From: Jerry Ebalunode <jebalunode@UH.EDU>
Subject: Re: namd-l: output warning in using namd2
 "Warning: Not all atoms have unique coordinates."
In-reply-to: <Pine.GSO.4.44.0309162112320.12166-100000@verdun.ks.uiuc.edu>
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Hi Jim,
Thanks. Commenting the CXXNOALIASOPTS  line helped in preventing this error 
warning. Thanks again.


On Wednesday 17 September 2003 02:19 am, Jim Phillips wrote:
> This error happens on every test simulation, and they used to work?  Hmmm.
> Your compiler and processor are both newer that what I've gotten to test
> at NCSA, and the "unique coordinates" warning really means that extra
> exclusions were calculated, which is very unusual.  You might want to back
> off on the optimization of ComputeNonbonded..., maybe start by commenting
> out CXXNOALIASOPTS from arch/Linux-ia64-ecc.arch.  If that eliminates the
> warning then we're at least on the right track (but Itanium is pretty
> pointless without those optimization flags).
>
> -Jim
>
> On Tue, 16 Sep 2003, Jerry Ebalunode wrote:
> > Hi all,
> > I just compiled namd2.5b2  on an itanium2 cluster that uses SCALI's
> > implementation of the mpi. When I run the binary, I always get this
> > warning "Warning: Not all atoms have unique coordinates." in the output
> > log.  Does anyone know how to correct this problem? I initially thought
> > it had to do with the tcl or fftw libraries I was using,  so used the
> > precompiled libraries from
> > http://www.ks.uiuc.edu/Research/namd/libraries/ meant for my
> > architecture. However, after recompiling and running namd2  I still had
> > the same problems.
> >
> >
> > Compiler information
> > intel C/C++ compiler  for itanium ecc version 7.1
> >
> > --
> > 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


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Date: Wed, 17 Sep 2003 12:54:46 +0000
From: Jerry Ebalunode <jebalunode@UH.EDU>
Subject: Re: namd-l: output warning in using namd2
 "Warning: Not all atoms have unique coordinates." more errors
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Hi Jim,
I got this removed this warning by taking blocking out the CXXO...  
optimization line. However I now have this new warning " BUG ALERT: Bad 
global exclusion count!"  and also this new warning when I turn on PME. 

OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Stray PME grid charges detected: 8 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 8 sending to 15 for planes 117 118 119
ERROR: Stray PME grid charges detected: 12 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 12 sending to 15 for planes 117 118 
119
ERROR: Stray PME grid charges detected: 6 sending to 15 for planes 117 118 119
ERROR: Stray PME grid charges detected: 16 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 15 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 13 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 14 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 11 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 11 sending to 15 for planes 117 118 
119
ERROR: Stray PME grid charges detected: 10 sending to 15 for planes 117 118 
119
ERROR: Stray PME grid charges detected: 10 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 9 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 9 sending to 15 for planes 117 118 119
ERROR: Stray PME grid charges detected: 7 sending to 15 for planes 117 118 119
ERROR: Stray PME grid charges detected: 7 sending to 3 for planes 0
ERROR: Stray PME grid charges detected: 5 sending to 15 for planes 117 118 119
ERROR: Stray PME grid charges detected: 4 sending to 15 for planes 117 118 119


 On Wednesday 17 September 2003 01:11 am, you wrote:
> Hi Jerry,
> I am running NAMD on linux debian and I get the same message.  I was
> using the older version 2.5b1 and someone suggest I try the new version
> 2.5b.  Now, I get a another warning Bad global exclusion count,
> possible error.  The previous version would end with segmentaion fault
> but this new version doesn't seg fault it just stalls at the same
> spot.  I have now narrowed it to a problem with the pdb or psf
> files...who knows if I'm correct, I've posted another meassage.  Other
> proteins I run do not give this problem which is why I think it might
> be pdb or psf.  Does your program work with other proteins or gives
> this on all you try?
> Cheers,
> Cheri
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Cheri M. Turman
>    Graduate Student
>    University of Texas-Houston Medical School
>     6431 Fannin
>     Houston, TX 77030
>
>     e-mail: cheri.m.turman@uth.tmc.edu
>     Ph.: 713-500-6126
>     Fax: 713-500-0652
>
> ----- Original Message -----
> From: Jerry Ebalunode <jebalunode@UH.EDU>
> Date: Tuesday, September 16, 2003 1:44 pm
> Subject: namd-l: output warning in using namd2 "Warning: Not all atoms
> have unique coordinates."
>
> > Hi all,
> > I just compiled namd2.5b2  on an itanium2 cluster that uses
> > SCALI's
> > implementation of the mpi. When I run the binary, I always get
> > this warning
> > "Warning: Not all atoms have unique coordinates." in the output
> > log.  Does
> > anyone know how to correct this problem? I initially thought it
> > had to do
> > with the tcl or fftw libraries I was using,  so used the
> > precompiled
> > libraries from http://www.ks.uiuc.edu/Research/namd/libraries/
> > meant for my
> > architecture. However, after recompiling and running namd2  I
> > still had the
> > same problems.
> >
> >
> > Compiler information
> > intel C/C++ compiler  for itanium ecc version 7.1
> >
> > --
> > 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 Wed Sep 17 13:07:49 2003
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Date: Wed, 17 Sep 2003 13:07:47 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: Jerry Ebalunode <jebalunode@UH.EDU>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: output warning in using namd2 "Warning: Not all atoms
 have unique coordinates." more errors
In-Reply-To: <200309171254.46164.jebalunode@uh.edu>
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What system is this running?  Does it happen with the apoa1 benchmark at
http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz ?

Both of these errors indicate a breakdown of NAMD's spatial decomposition,
either due to simulation instability or possibly some data corruption.

-Jim

On Wed, 17 Sep 2003, Jerry Ebalunode wrote:

> Hi Jim,
> I got this removed this warning by taking blocking out the CXXO...
> optimization line. However I now have this new warning " BUG ALERT: Bad
> global exclusion count!"  and also this new warning when I turn on PME.
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> ERROR: Stray PME grid charges detected: 8 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 8 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 12 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 12 sending to 15 for planes 117 118
> 119
> ERROR: Stray PME grid charges detected: 6 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 16 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 15 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 13 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 14 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 11 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 11 sending to 15 for planes 117 118
> 119
> ERROR: Stray PME grid charges detected: 10 sending to 15 for planes 117 118
> 119
> ERROR: Stray PME grid charges detected: 10 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 9 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 9 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 7 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 7 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 5 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 4 sending to 15 for planes 117 118 119
>
>
>  On Wednesday 17 September 2003 01:11 am, you wrote:
> > Hi Jerry,
> > I am running NAMD on linux debian and I get the same message.  I was
> > using the older version 2.5b1 and someone suggest I try the new version
> > 2.5b.  Now, I get a another warning Bad global exclusion count,
> > possible error.  The previous version would end with segmentaion fault
> > but this new version doesn't seg fault it just stalls at the same
> > spot.  I have now narrowed it to a problem with the pdb or psf
> > files...who knows if I'm correct, I've posted another meassage.  Other
> > proteins I run do not give this problem which is why I think it might
> > be pdb or psf.  Does your program work with other proteins or gives
> > this on all you try?
> > Cheers,
> > Cheri
> >
> >
> >
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >    Cheri M. Turman
> >    Graduate Student
> >    University of Texas-Houston Medical School
> >     6431 Fannin
> >     Houston, TX 77030
> >
> >     e-mail: cheri.m.turman@uth.tmc.edu
> >     Ph.: 713-500-6126
> >     Fax: 713-500-0652
> >
> > ----- Original Message -----
> > From: Jerry Ebalunode <jebalunode@UH.EDU>
> > Date: Tuesday, September 16, 2003 1:44 pm
> > Subject: namd-l: output warning in using namd2 "Warning: Not all atoms
> > have unique coordinates."
> >
> > > Hi all,
> > > I just compiled namd2.5b2  on an itanium2 cluster that uses
> > > SCALI's
> > > implementation of the mpi. When I run the binary, I always get
> > > this warning
> > > "Warning: Not all atoms have unique coordinates." in the output
> > > log.  Does
> > > anyone know how to correct this problem? I initially thought it
> > > had to do
> > > with the tcl or fftw libraries I was using,  so used the
> > > precompiled
> > > libraries from http://www.ks.uiuc.edu/Research/namd/libraries/
> > > meant for my
> > > architecture. However, after recompiling and running namd2  I
> > > still had the
> > > same problems.
> > >
> > >
> > > Compiler information
> > > intel C/C++ compiler  for itanium ecc version 7.1
> > >
> > > --
> > > 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 Thu Sep 18 15:25:24 2003
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From: "Saladino, Alex" <saladinoac@upmc.edu>
To: "'namd-l@ks.uiuc.edu'" <namd-l@ks.uiuc.edu>
Subject: namd-l: Minimization Question
Date: Thu, 18 Sep 2003 16:25:08 -0400
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Hello fellow NAMDers,
I have a question about minimizations. 
How do you know when your system has fully minimized?
Do people look at change in energies, absolute or relative? If not, what
else should I be looking at?


Thank you,
Alex



*************************************
Alexander C. Saladino, PhD
Department of Anesthesiology
University of Pittsburgh
*************************************
 

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<P><FONT SIZE=2 FACE="Arial">Hello fellow NAMDers,</FONT>
<BR><FONT SIZE=2 FACE="Arial">I have a question about minimizations. </FONT>
<BR><FONT SIZE=2 FACE="Arial">How do you know when your system has fully minimized?</FONT>
<BR><FONT SIZE=2 FACE="Arial">Do people look at change in energies, absolute or relative? If not, what else should I be looking at?</FONT>
</P>
<BR>

<P><FONT SIZE=2 FACE="Arial">Thank you,</FONT>
<BR><FONT SIZE=2 FACE="Arial">Alex</FONT>
</P>
<BR>
<BR>

<P><FONT SIZE=2 FACE="Arial">*************************************</FONT>
<BR><FONT SIZE=2 FACE="Arial">Alexander C. Saladino, PhD</FONT>
<BR><FONT SIZE=2 FACE="Arial">Department of Anesthesiology</FONT>
<BR><FONT SIZE=2 FACE="Arial">University of Pittsburgh</FONT>
<BR><FONT SIZE=2 FACE="Arial">*************************************</FONT>
<BR><FONT SIZE=2 FACE="Arial">&nbsp;</FONT>
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From owner-namd-l@rama.ks.uiuc.edu Thu Sep 18 16:30:51 2003
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From: Jim Phillips <jim@ks.uiuc.edu>
To: "Saladino, Alex" <saladinoac@upmc.edu>
cc: "'namd-l@ks.uiuc.edu'" <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: Minimization Question
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You'll wait a long time for minimization to converge for a large system,
and even then you're only guaranteed a local minimum.  Minimization is
normally used before starting MD to eliminate bad contacts and initial
heating.  I'd suggest plotting energy vs step and looking for diminishing
returns, or figuring out how many steps you're willing to wait.  1000
steps goes a long way and 10,000 should be sufficient for most systems.

-Jim


On Thu, 18 Sep 2003, Saladino, Alex wrote:

> Hello fellow NAMDers,
> I have a question about minimizations.
> How do you know when your system has fully minimized?
> Do people look at change in energies, absolute or relative? If not, what
> else should I be looking at?
>
>
> Thank you,
> Alex
>
>
>
> *************************************
> Alexander C. Saladino, PhD
> Department of Anesthesiology
> University of Pittsburgh
> *************************************
>
>


From owner-namd-l@rama.ks.uiuc.edu Fri Sep 19 18:03:00 2003
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Date: Fri, 19 Sep 2003 18:02:58 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: namd-l@ks.uiuc.edu
cc: vmd-l@ks.uiuc.edu
Subject: namd-l: NAMD 2.5b3 Released
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Hi,

This is the second NAMD release this week, and fixes a couple of bugs in
2.5b2.  I'm planning to have 2.5 final out by the end of the month (when
NCSA yanks the Origin 2000s away), so please give this a good thrashing.

NAMD users, please note the new NamdTroubleshooting page on the NAMD Wiki:

  http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting

People reading this on VMD-L, please also note the existence of NAMD-L.

Thanks!

-Jim


+--------------------------------------------------------------------+
|                                                                    |
|                  NAMD 2.5b3 Release Announcement                   |
|                                                                    |
+--------------------------------------------------------------------+

                                                  September 19, 2003

The Theoretical and Computational Biophysics Group at the University of
Illinois is proud to announce the public release of a new version of
NAMD, a parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems.  NAMD is
distributed free of charge and includes source code.  NAMD development
is supported by the NIH National Center for Research Resources.

NAMD 2.5b3 has several advantages over NAMD 2.4:

- Improved parallel scaling and serial performance.

- Trajectory reading and interaction energy analysis.

- Improved constant pressure simulation and coordinate wrapping.

NAMD is available from http://www.ks.uiuc.edu/Research/namd/.

For your convenience, NAMD has been ported to and will be installed
on the machines at the NSF-sponsored national supercomputing centers.
If you are planning substantial simulation work of an academic nature
you should apply for these resources.  Benchmarks for your proposal
are available at http://www.ks.uiuc.edu/Research/namd/performance.html

The Theoretical and Computational Biophysics Group encourages NAMD users
to be closely involved in the development process through reporting
bugs, contributing fixes, periodical surveys and via other means.
Questions or comments may be directed to namd@ks.uiuc.edu.

We are eager to hear from you, and thank you for using our software!




From owner-namd-l@rama.ks.uiuc.edu Sat Sep 20 15:02:46 2003
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Date: Sat, 20 Sep 2003 12:01:18 -0400
From: Amit Paliwal <paliwal@jhu.edu>
Subject: namd-l: hard sphere simulation
To: namd-l@ks.uiuc.edu
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Hi All,
What is the best way to incorporate a hard sphere in a simulation?
thanks,
Amit.


From owner-namd-l@rama.ks.uiuc.edu Mon Sep 22 14:38:13 2003
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From: Jim Phillips <jim@ks.uiuc.edu>
To: Amit Paliwal <paliwal@jhu.edu>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: hard sphere simulation
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I'd suggest modeling it as a very stiff "soft" interaction.

If you want a single sphere, substantially larger than an atom and located
at a fixed location then you can probably adapt the spherical harmonic
boundary conditions code (src/ComputeSphericalBC.[Ch]) to implement
whatever hard-core potential (like (r-r_0)^(-12)) you want.

Otherwise, you'll need to be a little more specific in what you want.

-Jim


On Sat, 20 Sep 2003, Amit Paliwal wrote:

> Hi All,
> What is the best way to incorporate a hard sphere in a simulation?
> thanks,
> Amit.
>


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From: "Cheri M Turman" <Cheri.M.Turman@uth.tmc.edu>
To: Jim Phillips <jim@ks.uiuc.edu>
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Hi Jim,
You were right about the files I had sent you.  I had tried so many
things that I couldn't really tell what went with what.  However, I saw
the H coordinates as you said in the pdb file and all were 0. The seg
fault was due to these coordinates being 0.  I added guesscoor after the
apoprotein segment and heme segment as you suggested and the H then got
coordinates assigned.  The problem with this is that the heme is
distorted as seen in vmd or SPDBViewer.  My original psfgen had the
guesscoord at this spot which is why they worked before in namd.  But
when I tried to prevent the heme distortion, I didn't allow psfgen to
guees coordinates of the heme only the apoprotein.  This is when the 0.0
are generated for the H of the heme.  In the distorted heme, it appears
as if psfgen is putting hydrogens in a frame where the carbons in the
heme ring (not part of pyrrole rings, ie. CHC) are sharing the hydrogen
with the adjacent carbon in the pyrrole ring (ie. C4B).  There should be
a double bond between these two carbons anyway leaving CHC with no room
for an H.  I cannot figure out why this is occuring.  Also, all other H
(ie. on methyl groups) also form bonds to each other.  These are both
puzzling me.  I have just started to manually modify the H to prevent
these bonds in the viewers.  Does anyone have comments on these problems?

Also, Jim, I am trying to run your namdplot script but I keep getting
syntax errors.  I had to change /bin/csh to /bin/bash so I was wondering
if my interpreter is not understanding the syntax.  I run Debian and the
bash is suppose to read also csh.  The error looked like this:

./namdplot: line 37: syntax error near unexpected token `('
./namdplot: line 37: `  foreach t ( $titles )'

Removing the "()" got me further down the program but I had to keep
removing these.  Finally, at the end it doesn't like how the file ends
so I get this error:

./namdplot: line 140: syntax error: unexpected end of file

Please let me know your thoughts...should I install an original csh?

Thanks,
Cheri

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030

    e-mail: cheri.m.turman@uth.tmc.edu
    Ph.: 713-500-6126
    Fax: 713-500-0652


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From owner-namd-l@rama.ks.uiuc.edu Mon Sep 22 18:20:22 2003
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Date: Mon, 22 Sep 2003 18:20:20 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: Cheri M Turman <Cheri.M.Turman@uth.tmc.edu>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: Re: seg fault and namdplot problem
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Hi Cheri,

First, psfgen guesses H positions based on the IC records in the topology
file or, failing that (since there are no IC records for H atoms in the
top_all22_prot.inp HEME residue), with some very crude rules assuming a
tetrahedral configuration.  The goal is to get close enough for the
minimizer to work.  If you use VMD with both the psf and pdb files you'll
see the real bonds, but don't make any single-bond assumptions based on
the initial geometry.

Regarding namdplot, bash has a very different syntax than csh (bash is
compatible with sh, but only steals features from ksh and csh).  If you
don't have csh you may have tcsh.  If it's not in /bin try /usr/bin/ or
/usr/local/bin (or the unix trick "/bin/env tcsh").

-Jim


On Mon, 22 Sep 2003, Cheri M Turman wrote:

> Hi Jim,
> You were right about the files I had sent you.  I had tried so many
> things that I couldn't really tell what went with what.  However, I saw
> the H coordinates as you said in the pdb file and all were 0. The seg
> fault was due to these coordinates being 0.  I added guesscoor after the
> apoprotein segment and heme segment as you suggested and the H then got
> coordinates assigned.  The problem with this is that the heme is
> distorted as seen in vmd or SPDBViewer.  My original psfgen had the
> guesscoord at this spot which is why they worked before in namd.  But
> when I tried to prevent the heme distortion, I didn't allow psfgen to
> guees coordinates of the heme only the apoprotein.  This is when the 0.0
> are generated for the H of the heme.  In the distorted heme, it appears
> as if psfgen is putting hydrogens in a frame where the carbons in the
> heme ring (not part of pyrrole rings, ie. CHC) are sharing the hydrogen
> with the adjacent carbon in the pyrrole ring (ie. C4B).  There should be
> a double bond between these two carbons anyway leaving CHC with no room
> for an H.  I cannot figure out why this is occuring.  Also, all other H
> (ie. on methyl groups) also form bonds to each other.  These are both
> puzzling me.  I have just started to manually modify the H to prevent
> these bonds in the viewers.  Does anyone have comments on these problems?
>
> Also, Jim, I am trying to run your namdplot script but I keep getting
> syntax errors.  I had to change /bin/csh to /bin/bash so I was wondering
> if my interpreter is not understanding the syntax.  I run Debian and the
> bash is suppose to read also csh.  The error looked like this:
>
> ./namdplot: line 37: syntax error near unexpected token `('
> ./namdplot: line 37: `  foreach t ( $titles )'
>
> Removing the "()" got me further down the program but I had to keep
> removing these.  Finally, at the end it doesn't like how the file ends
> so I get this error:
>
> ./namdplot: line 140: syntax error: unexpected end of file
>
> Please let me know your thoughts...should I install an original csh?
>
> Thanks,
> Cheri
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Cheri M. Turman
>    Graduate Student
>    University of Texas-Houston Medical School
>     6431 Fannin
>     Houston, TX 77030
>
>     e-mail: cheri.m.turman@uth.tmc.edu
>     Ph.: 713-500-6126
>     Fax: 713-500-0652
>
>


From owner-namd-l@rama.ks.uiuc.edu Mon Sep 22 18:58:37 2003
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From: "Cheri M Turman" <Cheri.M.Turman@uth.tmc.edu>
To: Jim Phillips <jim@ks.uiuc.edu>
Cc: namd-l@ks.uiuc.edu
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Thanks for the last commments, Jim.  I ended up installing csh. 
However, new problem...sorry to be such a bother, but I started using
xmgrace which is the new version of xmgr and the plotting would freeze
up not plotting anything/nothing in temp file created.  I figured your
namdplot was written for the older version of xmgr so I went and found 
4.1.2-10.  Now, I get xmgr to open, give the filename as title, put TS
as default on x axis, but nothing on y axis.  The terminal gives:
Read ended, non-numeric found on line at or near beginning of file.
Have you used your script with the newer versions of namd?  Do you have
quick hint on how to change the namdplot script to account for the
header generated in the namd logfile?  I also wonder if xmgr doesn't
like the initial step, gradient tolerance and bracket terms produced
intermittently in the logfile?  Thanks for the tips!
Cheers,
Cheri
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030

    e-mail: cheri.m.turman@uth.tmc.edu
    Ph.: 713-500-6126
    Fax: 713-500-0652

----- Original Message -----
From: Jim Phillips <jim@ks.uiuc.edu>
Date: Monday, September 22, 2003 6:20 pm
Subject: Re: namd-l: Re: seg fault and namdplot problem

> Hi Cheri,
> 
> First, psfgen guesses H positions based on the IC records in the 
> topologyfile or, failing that (since there are no IC records for H 
> atoms in the
> top_all22_prot.inp HEME residue), with some very crude rules 
> assuming a
> tetrahedral configuration.  The goal is to get close enough for the
> minimizer to work.  If you use VMD with both the psf and pdb files 
> you'llsee the real bonds, but don't make any single-bond 
> assumptions based on
> the initial geometry.
> 
> Regarding namdplot, bash has a very different syntax than csh (bash is
> compatible with sh, but only steals features from ksh and csh).  If 
> youdon't have csh you may have tcsh.  If it's not in /bin try 
> /usr/bin/ or
> /usr/local/bin (or the unix trick "/bin/env tcsh").
> 
> -Jim
> 
> 
> On Mon, 22 Sep 2003, Cheri M Turman wrote:
> 
> > Hi Jim,
> > You were right about the files I had sent you.  I had tried so many
> > things that I couldn't really tell what went with what.  However, 
> I saw
> > the H coordinates as you said in the pdb file and all were 0. The 
> seg> fault was due to these coordinates being 0.  I added guesscoor 
> after the
> > apoprotein segment and heme segment as you suggested and the H 
> then got
> > coordinates assigned.  The problem with this is that the heme is
> > distorted as seen in vmd or SPDBViewer.  My original psfgen had the
> > guesscoord at this spot which is why they worked before in namd.  
> But> when I tried to prevent the heme distortion, I didn't allow 
> psfgen to
> > guees coordinates of the heme only the apoprotein.  This is when 
> the 0.0
> > are generated for the H of the heme.  In the distorted heme, it 
> appears> as if psfgen is putting hydrogens in a frame where the 
> carbons in the
> > heme ring (not part of pyrrole rings, ie. CHC) are sharing the 
> hydrogen> with the adjacent carbon in the pyrrole ring (ie. C4B).  
> There should be
> > a double bond between these two carbons anyway leaving CHC with 
> no room
> > for an H.  I cannot figure out why this is occuring.  Also, all 
> other H
> > (ie. on methyl groups) also form bonds to each other.  These are 
> both> puzzling me.  I have just started to manually modify the H to 
> prevent> these bonds in the viewers.  Does anyone have comments on 
> these problems?
> >
> > Also, Jim, I am trying to run your namdplot script but I keep 
> getting> syntax errors.  I had to change /bin/csh to /bin/bash so I 
> was wondering
> > if my interpreter is not understanding the syntax.  I run Debian 
> and the
> > bash is suppose to read also csh.  The error looked like this:
> >
> > ./namdplot: line 37: syntax error near unexpected token `('
> > ./namdplot: line 37: `  foreach t ( $titles )'
> >
> > Removing the "()" got me further down the program but I had to keep
> > removing these.  Finally, at the end it doesn't like how the file 
> ends> so I get this error:
> >
> > ./namdplot: line 140: syntax error: unexpected end of file
> >
> > Please let me know your thoughts...should I install an original csh?
> >
> > Thanks,
> > Cheri
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >    Cheri M. Turman
> >    Graduate Student
> >    University of Texas-Houston Medical School
> >     6431 Fannin
> >     Houston, TX 77030
> >
> >     e-mail: cheri.m.turman@uth.tmc.edu
> >     Ph.: 713-500-6126
> >     Fax: 713-500-0652
> >
> >
> 
> 

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Date: Mon, 22 Sep 2003 21:08:31 -0400
From: AMIT PALIWAL <paliwal@jhu.edu>
Subject: Re: namd-l: hard sphere simulation
To: namd-l@ks.uiuc.edu
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Hi,
Jim ...good to hear from you!
regrading the specifics..i want to simulate a very large ( say a 5 or 10 ang. radius) hard sphere in water. Can i implement a step function type potential ( infinity if r < r0 and zero otherwise) ?
I have never implemented spherical boundary conditions before...are their any examples anywhere?   
thanks,
Amit.

----- Original Message -----
From: Jim Phillips <jim@ks.uiuc.edu>
Date: Monday, September 22, 2003 3:38 pm
Subject: Re: namd-l: hard sphere simulation

> 
> I'd suggest modeling it as a very stiff "soft" interaction.
> 
> If you want a single sphere, substantially larger than an atom and 
> locatedat a fixed location then you can probably adapt the 
> spherical harmonic
> boundary conditions code (src/ComputeSphericalBC.[Ch]) to implement
> whatever hard-core potential (like (r-r_0)^(-12)) you want.
> 
> Otherwise, you'll need to be a little more specific in what you want.
> 
> -Jim
> 
> 
> On Sat, 20 Sep 2003, Amit Paliwal wrote:
> 
> > Hi All,
> > What is the best way to incorporate a hard sphere in a simulation?
> > thanks,
> > Amit.
> >
> 
> 


From owner-namd-l@rama.ks.uiuc.edu Mon Sep 22 20:53:33 2003
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From: "Liu, Zhanwu" <LiuxZx@anes.upmc.edu>
To: "'Jim Phillips '" <jim@ks.uiuc.edu>
Cc: "'namd-l@ks.uiuc.edu'" <namd-l@ks.uiuc.edu>
Subject: namd-l: coorfile command fail
Date: Mon, 22 Sep 2003 21:53:13 -0400
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Dear Jim,

I am trying to use the new command "coorfile" to analyze trajectories, 
but it seems like doesn't working in my case. Part of the output file
is enclosed. Do you have any idea where the error come from?

Thanks 

Yours Zhanwu

Zhanwu Liu, Ph.D.
Department of Anesthesiology
University of Pittsburgh
==========================


Info: Entering startup phase 0 with 7865 kB of memory in use.
Info: Entering startup phase 1 with 7865 kB of memory in use.
Info: Entering startup phase 2 with 10503 kB of memory in use.
Info: Entering startup phase 3 with 10753 kB of memory in use.
Info: PATCH GRID IS 3 (PERIODIC) BY 2 (PERIODIC) BY 3 (PERIODIC)
Info: REMOVING COM VELOCITY 0 0 0
Info: LARGEST PATCH (0) HAS 944 ATOMS
Info: Entering startup phase 4 with 13246 kB of memory in use.
Info: Entering startup phase 5 with 13246 kB of memory in use.
Info: Entering startup phase 6 with 13246 kB of memory in use.
Info: Entering startup phase 7 with 13247 kB of memory in use.
Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
Info: COULOMB TABLE SIZE: 769 POINTS
Info: NONZERO IMPRECISION IN COULOMB TABLE: 0 (0) 6.31089e-30 (712)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 0 (0) 7.7755e-23 (712)
Info: Entering startup phase 8 with 17739 kB of memory in use.
Info: Finished startup with 20177 kB of memory in use.
read_dcdreader returned -6
TCL: coorfile: Error opening file /tmp/zliu4/test.dcd
FATAL ERROR: coorfile: Error opening file /tmp/zliu4/test.dcd
    while executing
"coorfile open dcd "/tmp/zliu4/test.dcd""
    (file "AnalysisScript.conf" line 45)
FATAL ERROR: coorfile: Error opening file /tmp/zliu4/test.dcd
    while executing
"coorfile open dcd "/tmp/zliu4/test.dcd""
    (file "AnalysisScript.conf" line 45)

From owner-namd-l@rama.ks.uiuc.edu Tue Sep 23 10:52:15 2003
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Date: Tue, 23 Sep 2003 10:52:14 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: AMIT PALIWAL <paliwal@jhu.edu>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: hard sphere simulation
In-Reply-To: <55056154efd1.54efd1550561@jhumail.jhu.edu>
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If your sphere is hard but the other atoms are not, then you really have a
soft potential using the VDW radii of the other atoms.  Depending on what
you are actually trying to model, you might consider putting together an
appropriately sized fullerene to act as a sphere.  What are you trying to
accomplish?

-Jim

On Mon, 22 Sep 2003, AMIT PALIWAL wrote:

> Hi, Jim ...good to hear from you! regrading the specifics..i want to
> simulate a very large ( say a 5 or 10 ang. radius) hard sphere in water.
> Can i implement a step function type potential ( infinity if r < r0 and
> zero otherwise) ? I have never implemented spherical boundary conditions
> before...are their any examples anywhere?  thanks, Amit.
>
> ----- Original Message -----
> From: Jim Phillips <jim@ks.uiuc.edu>
> Date: Monday, September 22, 2003 3:38 pm
> Subject: Re: namd-l: hard sphere simulation
>
> >
> > I'd suggest modeling it as a very stiff "soft" interaction.
> >
> > If you want a single sphere, substantially larger than an atom and
> > locatedat a fixed location then you can probably adapt the
> > spherical harmonic
> > boundary conditions code (src/ComputeSphericalBC.[Ch]) to implement
> > whatever hard-core potential (like (r-r_0)^(-12)) you want.
> >
> > Otherwise, you'll need to be a little more specific in what you want.
> >
> > -Jim
> >
> >
> > On Sat, 20 Sep 2003, Amit Paliwal wrote:
> >
> > > Hi All,
> > > What is the best way to incorporate a hard sphere in a simulation?
> > > thanks,
> > > Amit.
> > >
> >
> >
>


From owner-namd-l@rama.ks.uiuc.edu Tue Sep 23 11:20:14 2003
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Date: Tue, 23 Sep 2003 11:20:13 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: "Liu, Zhanwu" <LiuxZx@anes.upmc.edu>
cc: "'namd-l@ks.uiuc.edu'" <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: coorfile command fail
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Hi,

Digging through the plugins source code...

First, read_dcdreader is a typo, it should be read_dcdheader, and...

#define DCD_EOF         -1  /*  Normal EOF                          */
#define DCD_DNE         -2  /*  DCD file does not exist             */
#define DCD_OPENFAILED  -3  /*  Open of DCD file failed             */
#define DCD_BADREAD     -4  /*  read call on DCD file failed        */
#define DCD_BADEOF      -5  /*  premature EOF found in DCD file     */
#define DCD_BADFORMAT   -6  /*  format of DCD file is wrong         */
#define DCD_FILEEXISTS  -7  /*  output file already exists          */
#define DCD_BADMALLOC   -8  /*  malloc failed

So, the format is wrong somehow.  Try loading this DCD file in VMD.  If it
doesn't work in VMD then there is probably something wrong with the file.

-Jim


On Mon, 22 Sep 2003, Liu, Zhanwu wrote:

> Dear Jim,
>
> I am trying to use the new command "coorfile" to analyze trajectories,
> but it seems like doesn't working in my case. Part of the output file
> is enclosed. Do you have any idea where the error come from?
>
> Thanks
>
> Yours Zhanwu
>
> Zhanwu Liu, Ph.D.
> Department of Anesthesiology
> University of Pittsburgh
> ==========================
>
>
> Info: Entering startup phase 0 with 7865 kB of memory in use.
> Info: Entering startup phase 1 with 7865 kB of memory in use.
> Info: Entering startup phase 2 with 10503 kB of memory in use.
> Info: Entering startup phase 3 with 10753 kB of memory in use.
> Info: PATCH GRID IS 3 (PERIODIC) BY 2 (PERIODIC) BY 3 (PERIODIC)
> Info: REMOVING COM VELOCITY 0 0 0
> Info: LARGEST PATCH (0) HAS 944 ATOMS
> Info: Entering startup phase 4 with 13246 kB of memory in use.
> Info: Entering startup phase 5 with 13246 kB of memory in use.
> Info: Entering startup phase 6 with 13246 kB of memory in use.
> Info: Entering startup phase 7 with 13247 kB of memory in use.
> Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
> Info: COULOMB TABLE SIZE: 769 POINTS
> Info: NONZERO IMPRECISION IN COULOMB TABLE: 0 (0) 6.31089e-30 (712)
> Info: NONZERO IMPRECISION IN COULOMB TABLE: 0 (0) 7.7755e-23 (712)
> Info: Entering startup phase 8 with 17739 kB of memory in use.
> Info: Finished startup with 20177 kB of memory in use.
> read_dcdreader returned -6
> TCL: coorfile: Error opening file /tmp/zliu4/test.dcd
> FATAL ERROR: coorfile: Error opening file /tmp/zliu4/test.dcd
>     while executing
> "coorfile open dcd "/tmp/zliu4/test.dcd""
>     (file "AnalysisScript.conf" line 45)
> FATAL ERROR: coorfile: Error opening file /tmp/zliu4/test.dcd
>     while executing
> "coorfile open dcd "/tmp/zliu4/test.dcd""
>     (file "AnalysisScript.conf" line 45)
>


From owner-namd-l@rama.ks.uiuc.edu Tue Sep 23 21:44:26 2003
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Date: Tue, 23 Sep 2003 21:44:24 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: Cheri M Turman <Cheri.M.Turman@uth.tmc.edu>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: Re: seg fault and namdplot problem
In-Reply-To: <149db10a5a.10a5a149db@uth.tmc.edu>
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Hi,

I just added a newer Grace-based namdplot as well as namdstats and
namdpstats (which print energy and pressure statistics) to

  http://www.ks.uiuc.edu/Research/namd/utilities/

These also add [from <first>] and [to <last>] options so you can plot or
analyze a segment of the file, such as skipping equilibration.

-Jim


On Mon, 22 Sep 2003, Cheri M Turman wrote:

> Thanks for the last commments, Jim.  I ended up installing csh.
> However, new problem...sorry to be such a bother, but I started using
> xmgrace which is the new version of xmgr and the plotting would freeze
> up not plotting anything/nothing in temp file created.  I figured your
> namdplot was written for the older version of xmgr so I went and found
> 4.1.2-10.  Now, I get xmgr to open, give the filename as title, put TS
> as default on x axis, but nothing on y axis.  The terminal gives:
> Read ended, non-numeric found on line at or near beginning of file.
> Have you used your script with the newer versions of namd?  Do you have
> quick hint on how to change the namdplot script to account for the
> header generated in the namd logfile?  I also wonder if xmgr doesn't
> like the initial step, gradient tolerance and bracket terms produced
> intermittently in the logfile?  Thanks for the tips!
> Cheers,
> Cheri
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Cheri M. Turman
>    Graduate Student
>    University of Texas-Houston Medical School
>     6431 Fannin
>     Houston, TX 77030
>
>     e-mail: cheri.m.turman@uth.tmc.edu
>     Ph.: 713-500-6126
>     Fax: 713-500-0652
>
> ----- Original Message -----
> From: Jim Phillips <jim@ks.uiuc.edu>
> Date: Monday, September 22, 2003 6:20 pm
> Subject: Re: namd-l: Re: seg fault and namdplot problem
>
> > Hi Cheri,
> >
> > First, psfgen guesses H positions based on the IC records in the
> > topologyfile or, failing that (since there are no IC records for H
> > atoms in the
> > top_all22_prot.inp HEME residue), with some very crude rules
> > assuming a
> > tetrahedral configuration.  The goal is to get close enough for the
> > minimizer to work.  If you use VMD with both the psf and pdb files
> > you'llsee the real bonds, but don't make any single-bond
> > assumptions based on
> > the initial geometry.
> >
> > Regarding namdplot, bash has a very different syntax than csh (bash is
> > compatible with sh, but only steals features from ksh and csh).  If
> > youdon't have csh you may have tcsh.  If it's not in /bin try
> > /usr/bin/ or
> > /usr/local/bin (or the unix trick "/bin/env tcsh").
> >
> > -Jim
> >
> >
> > On Mon, 22 Sep 2003, Cheri M Turman wrote:
> >
> > > Hi Jim,
> > > You were right about the files I had sent you.  I had tried so many
> > > things that I couldn't really tell what went with what.  However,
> > I saw
> > > the H coordinates as you said in the pdb file and all were 0. The
> > seg> fault was due to these coordinates being 0.  I added guesscoor
> > after the
> > > apoprotein segment and heme segment as you suggested and the H
> > then got
> > > coordinates assigned.  The problem with this is that the heme is
> > > distorted as seen in vmd or SPDBViewer.  My original psfgen had the
> > > guesscoord at this spot which is why they worked before in namd.
> > But> when I tried to prevent the heme distortion, I didn't allow
> > psfgen to
> > > guees coordinates of the heme only the apoprotein.  This is when
> > the 0.0
> > > are generated for the H of the heme.  In the distorted heme, it
> > appears> as if psfgen is putting hydrogens in a frame where the
> > carbons in the
> > > heme ring (not part of pyrrole rings, ie. CHC) are sharing the
> > hydrogen> with the adjacent carbon in the pyrrole ring (ie. C4B).
> > There should be
> > > a double bond between these two carbons anyway leaving CHC with
> > no room
> > > for an H.  I cannot figure out why this is occuring.  Also, all
> > other H
> > > (ie. on methyl groups) also form bonds to each other.  These are
> > both> puzzling me.  I have just started to manually modify the H to
> > prevent> these bonds in the viewers.  Does anyone have comments on
> > these problems?
> > >
> > > Also, Jim, I am trying to run your namdplot script but I keep
> > getting> syntax errors.  I had to change /bin/csh to /bin/bash so I
> > was wondering
> > > if my interpreter is not understanding the syntax.  I run Debian
> > and the
> > > bash is suppose to read also csh.  The error looked like this:
> > >
> > > ./namdplot: line 37: syntax error near unexpected token `('
> > > ./namdplot: line 37: `  foreach t ( $titles )'
> > >
> > > Removing the "()" got me further down the program but I had to keep
> > > removing these.  Finally, at the end it doesn't like how the file
> > ends> so I get this error:
> > >
> > > ./namdplot: line 140: syntax error: unexpected end of file
> > >
> > > Please let me know your thoughts...should I install an original csh?
> > >
> > > Thanks,
> > > Cheri
> > >
> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > >    Cheri M. Turman
> > >    Graduate Student
> > >    University of Texas-Houston Medical School
> > >     6431 Fannin
> > >     Houston, TX 77030
> > >
> > >     e-mail: cheri.m.turman@uth.tmc.edu
> > >     Ph.: 713-500-6126
> > >     Fax: 713-500-0652
> > >
> > >
> >
> >
>


From owner-namd-l@rama.ks.uiuc.edu Wed Sep 24 12:55:24 2003
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Date: Wed, 24 Sep 2003 18:53:28 +0100 (BST)
From: james tomomi macdonald <j.macdonald@mail.cryst.bbk.ac.uk>
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Hi,

Are there any plans to introduce implicit solvent methods such as 
generalised born to NAMD?

Cheers,

James.



From owner-namd-l@rama.ks.uiuc.edu Wed Sep 24 14:09:16 2003
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Date: Wed, 24 Sep 2003 14:09:14 -0500 (CDT)
From: Jim Phillips <jim@ks.uiuc.edu>
To: james tomomi macdonald <j.macdonald@mail.cryst.bbk.ac.uk>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: implicit solvent models
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There are plans, but nothing specific yet.  Feel free to add your comments
and suggestions on the wiki at
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdRequests

-Jim


On Wed, 24 Sep 2003, james tomomi macdonald wrote:

>
> Hi,
>
> Are there any plans to introduce implicit solvent methods such as
> generalised born to NAMD?
>
> Cheers,
>
> James.
>
>


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Date: Wed, 24 Sep 2003 20:12:14 -0400
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Subject: namd-l: Launching namd with PBS
From: Scott Stagg <scott.stagg@biology.gatech.edu>
To: namd-l@ks.uiuc.edu
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Hi all,
   I have been using namd successfully on my local Linux cluster for 
several months, but now we are looking to implement a batch queue 
system. We are trying to use PBS but I am having problems with the 
nodelist file. Basically charmrun overrides PBS in choosing the nodes 
namd runs on. The point a batch queue though is so users don't have to 
choose the nodes on which they run. Has anyone run into this problem? 
Any suggestions on what I should do?

Thanks,
Scott Stagg

From owner-namd-l@rama.ks.uiuc.edu Wed Sep 24 19:17:50 2003
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