[gmx-users] Re: compressing the system

Vitaly Chaban vvchaban at gmail.com
Fri Jul 30 12:49:30 CEST 2010

Dear Moeed:

Please run the simulation with the same input files that I edited for
you. It is impossible to resolve any difficulty if you change the
parameters so vigorously. The equilibration stage should be rather
long for polymers, be always careful about that.

Be sure, the run was performed with 8 chains. But probably you did not
take your total energy per MOLE as I did (please see the designations
on my plot).


Dr. Vitaly Chaban

> Dear Dr.Vitaly Chaban
> I ran the simulation with PME for a short time ,36ps and noticed
> electrostatic energy is converging to a 1200 which is close to what I got
> with shift function. total enerfy is around 14000 which is very far from
> what you got. Kinetic energy per se is around 7000 while you obtained a
> total energy of 2000 Kj/mol. I am curious why results are not the same. Are
> you sure you did the simulation with 8 molecules and not with a single
> chain?
> Sorry to have bothered you..
> Moeed

More information about the gromacs.org_gmx-users mailing list