[gmx-users] minimization problem

[Paymon Pirzadeh]

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 at 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-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
>