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

Itamar Kass itamar.kass at monash.edu
Thu Aug 18 02:47:21 CEST 2011

Dear Mark,

We also tried to minimise the system in vacuum before adding water and ions withou, but it still crashed when we did MD.

On 18/08/2011, at 10:31 AM, Mark Abraham wrote:

> 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 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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"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu

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