[gmx-users] GROMACS 4.5.4 keep crashing all the time.

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 18 02:31:59 CEST 2011

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.neale at utoronto.ca <mailto:chris.neale at 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? 

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