[Bulk] [gmx-users] a question about potential energy

Yang Ye leafyoung at yahoo.com
Sat Aug 11 05:41:35 CEST 2007


You shall help yourself to find the answer by plotting your energy with

Have your equilibrated your system well? Which stage of simulation are
you running with, em, eq or production run? Having large fluctuation is
sometimes normal and sometimes bad.

Also, please attach necessary and concise information to the mails. We
may open a table-like file (e.g. xvg) for energy but not a log file just
for energies. I understand that you could be new to gromacs, just take
note of this.

Yang Ye

On 8/10/2007 3:54 PM, taojinwuhan at sohu.com wrote:
> Hi, all
> I have found a problem that in my Md run the potential energy in every
> frame was about -9e+04 while the average potential energy of all was
> -1.88e+02. What is wrong with it? Why are they so different? Can
> anybody tell me the reason? Thanks!
> pS: the attachement is the md.log. You can clearly see that the
> average energy is so different with the energy in each frame in it.
> Paul
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