On 11/12/13 12:14 PM, cjalmeciga wrote:
The output of energy minimization was
Potential Energy = -1.42173622068236e+06
Maximum force = 9.00312066109319e+02 on atom 148
Norm of force = 2.06087515037187e+01
OK, reasonable enough. How about a description of what the system is, which
force field you chose, how you derived the ligand topology, and the full
contents of your .mdp file?
-Justin
Thanks
Javier
Justin Lemkul wrote
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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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul@.umaryland
| (410) 706-7441
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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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