Dear Justin, Thanks for the fast response. The exact command I used is :
mdrun -v -s eq2.tpr -deffnm eq2 -g eq2.log -nice 19 >& eq2.out & Regards, Ozlem On Wed, May 4, 2011 at 3:23 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Ozlem Ulucan wrote: > >> >> Dear Gromacs Users, >> >> I have been trying to simulate a protein in implicit solvent. When I used >> a single processor by setting -nt to 1 , I did not encounter any problem. >> But when I tried to run the simulations using more than 1 processor I get >> the following error. >> >> Fatal error: >> Constraint dependencies further away than next-neighbor >> in particle decomposition. Constraint between atoms 2177--2179 evaluated >> on node 3 and 3, but atom 2177 has connections within 4 bonds >> (lincs_order) >> of node 1, and atom 2179 has connections within 4 bonds of node 3. >> Reduce the # nodes, lincs_order, or >> try domain decomposition. >> >> I set the lincs_order parameter in .mdp file to different values. But it >> did not help. I have some questions regarding the information above. >> >> 1) Is it possible to run implicit solvent simulations in parallel? >> >> > Yes. > > > 2) As far as I know gromacs uses domain decomposition as default. Why >> does in my simulations gromacs use the particle decomposition which I do not >> ask for. >> >> > Without seeing the exact commands you gave, there is no plausible > explanation. DD is used by default. > > -Justin > > > Any suggestions are appreciated very much. >> I am ussing gromacs-4.5.4 with charmm force field and the OBC implicit >> solvent model. If you need further informations, probably a run input file, >> let me know. >> >> Regards, >> >> Ozlem Ulucan >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
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