On 11/12/13 10:58 AM, cjalmeciga wrote:
I run
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
and everything looks fine. I check the nvt.tpr, and temperature is ok.
The fact that grompp completes indicates there is nothing syntactically wrong
with the input files. Whether or not the content of the .mdp is physically
sensible or the input configuration is plausible is an entirely different
matter. Please tell us what the exact outcome of the previous energy
minimization was (potential energy, maximum force, copied and pasted from screen
output or .log file).
the real problem is with the mdrun function.
could be a problem of the software?
You have presented no evidence that would lead anyone to believe the problem is
with mdrun. In the vast majority of cases, user input is the problem.
-Justin
Thanks
Javier
Justin Lemkul wrote
On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:
Hello evryone,
I doing a simulation of a ligand-protein interaction with gromacs 4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex. I'm
running these commands:
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
mdrun -deffnm nvt
Nevertheless, I got this error:
"Reading file nvt.tpr, VERSION 4.5.5 (double precision)
Segmentation fault"
What should I do?
Instantaneous failure typically indicates that the forces are
nonsensically high
and the constraint algorithm immediately fails. Likely the previous
energy
minimization did not adequately complete.
-Justin
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Justin A. Lemkul, Ph.D.
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School of Pharmacy
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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