Sorry, That was a big typo(a mis-pasted line)!!!!! What is the suggestion anyway about emstep?
Payman On Mon, 2009-10-26 at 10:43 +1100, Itamar Kass wrote: > I am not sure what you refer to as dt, as there no meaning to time in > EM. > > Anyway, I think the easiest way is to remove this ware molecule. > > Best, > Itamar. > > On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote: > > > Hello, > > I merged two simulation boxes, and now I want to perform a > > minimization > > to remove the problems at their boundary! I have reduced the dt to > > 0.000000001 and emstep to 0.000000001 as well. But still I get the > > message > > Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double > > precision) > > Making 1D domain decomposition 8 x 1 x 1 > > Steepest Descents: > > Tolerance (Fmax) = 1.00000e-05 > > Number of steps = 705032704 > > > > t = 0.000 ps: Water molecule starting at atom 190501 can not be > > settled. > > Check for bad contacts and/or reduce the timestep. > > Wrote pdb files with previous and current coordinates > > > > ------------------------------------------------------- > > Program mdrun_d_mpi, VERSION 4.0.5 > > Source code file: pme.c, line: 518 > > > > Fatal error: > > 3 particles communicated to PME node 7 are more than a cell length out > > of the domain decomposition cell of their charge group > > > > as part of my error message. Should I still reduce the mentioned > > parameters? > > Regards, > > > > Payman > > > > _______________________________________________ > > 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 > > _______________________________________________ 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
