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.
Itamar. 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.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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----- "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.k...@monash.edu ============================================
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