Patricia Francis-Lyon wrote:
Hi, I'm new to gromacs and I can't figure out what I'm doing wrong
with parallel runs. I'm running gromacs 3.3.2 on a 215 residue protein:
1rz4.pdb. The 2 missing residues were added with modloop followed by
energy minimization. The protein was put in a dodecahedron box and
solvated with a layer of water at least 1.2 nm from the protein and 14
Na+ ions were added to bring the total charge of the system to zero.
Energy minimization was done to remove close contacts.
When I run on a single processor my MD runs seem fine (heatup position
restrained MD, constant temperature position restrained MD, and now the
production MD run is almost 86% complete). But when I run on a cluster
some I get strange fatal errors, maybe tripped by boolean checks during
writing of energy info to file. During position restrained MD I got:
fatal error in function do_enx (line 343 of enxio.c)
during the call:
gmx_fatal(FARGS,"could not write energies")
The fatal error happened after printing Coulomb1-4 energy in the log
file, the next line of headings was NOT printed.
During production run of MD I got:
Source code file: stat.c, line: 283
Fatal error: XTC error
This error usually means that either your box explodes, or your disk is
full. Could it be either of these problems?
If not, is it reproducible?
happening after writing these lines in the log:
Step Time Lambda
257600 515.20001 0.00000
These errors do not appear when I run equilibriation and production MD
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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