[gmx-users] potential energy of a peptide in explicit DMSO
feenstra at few.vu.nl
Tue Jul 26 10:14:16 CEST 2005
Xiaoming Zhang wrote:
> Dear users,
> I am running the MD simulation of a cyclic peptide in explicit DMSO.
> It is straightforward to retrieve the potential energy of the whole
> system (peptide + DMSO) using g_energy. However, I didn't find a way
> to calculate/retrieve the potential energy for the peptide only. I
> was wondering if any of you had the experience and knew how to deal
> with it.
You need to define energy groups in your mdp file before you perform the
simulation. Alternately, you can re-run your generated trajectory. See
manual for more details.
* NOTE: New Phone & Fax numbers (below) *
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
More information about the gromacs.org_gmx-users