On 18/08/2011 10:14 AM, Itamar Kass wrote:
Hi Chris and Justin,
On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
chris.ne...@utoronto.ca <mailto:chris.ne...@utoronto.ca> wrote:
You'll need to provide a much better report than this if you want to
receive any useful help.
Copy and paste the exact commands of what you did
Copy and paste the exact log file and error messages
The command I had used (for both 4.0.7 and 4.5.4) are:
pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp
editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic
genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top
-seed 5
grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr
genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname
CL- -np 17 -seed 66
grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr
mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g
1EXR_em.log -c 1EXR_em.gro
grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr
mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e
1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro
grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr
mpirun mdrun_d_mpi -v -stepout 10000 -s md.tpr -x 1EXR_md.xtc -e
1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro
So you're doing solvated EM, then position-restrained NPT MD, then NPT.
Sounds to me like you might have a bad initial contact that can't relax
under solvated EM, nor under PR-NPT, and is getting numerically lucky in
4.0.7 and not under 4.5.4. If so, then careful inspection of the start
of the 4.0.7 run might show this. Vacuo EM of the solute might help if
the problem is intra-solute. Have you explored the suggestions here?
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Mark
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