Jorge Alberto Jover Galtier wrote:
Hi, Justin.
Thank you for answering so quickly. We write you directly because we
receive the daily digest from Gromacs and we are not sure how to answer
to the thread. We have tried what you suggested, using 10,000 steps and
Reply to the message, strip out any unnecessary posts in the digest, and change
the subject line back to what you originally set it as (i.e., not "gmx-users
digest..."). I must insist that you keep all correspondence on the list so that
others can benefit from the conversation, and hopefully help out if necessary.
writing data every 100 steps, and we still have the same problem. The
protein we are using is a very small one, with 59 atoms, and we are
working in vacuum.
What about my suggestion for using g_traj -b and/or -e to write just a few
frames? This would be a far more useful test.
The only idea we have is that maybe we are making some mistakes at
generating the .gro and .top files. These are the instructions we are
using. From the .pdb file, we use:
Your problem is from an analysis tool, not from any of these files. Your
simulation successfully ran, but your analysis broke down. The only file worth
checking would be the .trr file (using gmxcheck), in case it was corrupted
during the run.
pdb2gmx -ignh -f pep.pdb -o pep.gro -p pep.top
We use the default force field and water model. And then we create the
box to the protein:
editconf -f pep.gro -d 0.7 -o pep_ini.gro
After that, we begin the simulations. We send you the files we are
working with, in case you want to try something. And if you have some
I don't have the means or reason to re-run your system from the start. As I
said, the problem is with an analysis tool, not the run itself.
If g_traj is still failing, please post a complete description of your hardware,
compilers, etc including all of the following:
1. Gromacs version
2. Compilers used (version is especially important)
3. Installation commands (configuration)
4. Hardware and OS
-Justin
other ideas, we would be really pleased to read them.
Thank you very much in advance and best wishes,
Jorge Alberto Jover Galtier
Universidad de Zaragoza, Spain
"Anuncia tu coche Gratis con AutoScout24"
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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