wuxiao wrote: > Dear Mark and Vitaly, > In order to get help, here I describe the more detailed procedure. > I successfully generated the gro and top files using pdb2gmx. > pdb2gmx -f -o -p -ter > And also the grompp finished successfully. > grompp -f -c -p -o > Then I ran the mdrun in parallel way, only to find that the polymer became > many pieces.
I doubt that it did. The representation of it that you were viewing may have made what was one topology look like many pieces. > mpirun -np 4 mpimdrun -s -o -c -e -g -v > Obviously, it cannot form any bonds between those pieces due to the long > distances. > With the same tpr file,I ran the mdrun in non-parallel-way, however, the > polymer seems to behave properly. > mdrun -s -o -c -e -g -v > The partial files (gro, top, and mdp) are given as follows: > > gro file: > Great Red Owns Many ACres of Sand > 1382 > 1DIA N1 1 -0.199 0.069 0.078 > ...... > 125AMI H42 1382 -0.073 -0.681 -1.613 > 3.61500 4.27230 2.77190 Since you are doing simulating a periodic system, are these box dimensions reasonable? Mark > top file: > ...... > [ molecules ] > ; Compounds #moles > Protein_D 1 > > mdp file: > ...... > define = -DFLEXIBLE > constraint = none > integrator = steep > nsteps = 10000 > ns_type = grid > nstcgsteep = 100 > nslist = 10 > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.0 > DispCorr = EnerPres > fourierspacing = 0.36 > pme_order = 4 > ewald_rtol = 1e-5 > emtol = 10 > emstep = 0.01 > > > > _________________________________________________________________ > 上Windows Live 中国首页，下载最新版Messenger！ > http://www.windowslive.cn > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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/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/mailing_lists/users.php _______________________________________________ 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/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/mailing_lists/users.php
