On 12/27/13, 6:00 PM, Ali Alizadeh wrote:
Dear All users,

I have a question about calculation of potential energy for an especial
group. I know I had to

define an energy group in .mdp file. I forgot to do it. I want to know can
I extract this potential

energy by post processing or not? If not this means I must perform my
simulation again?


There is no .mdp option to calculate the potential energy of just a single group. One can excluded nonbonded interactions between pairs of groups or decompose nonbonded energy between pairs of groups.

One could obtain "the potential energy of a group" by stripping out the coordinates of interest from the original trajectory (with trjconv), making a matching .tpr file (with tpbconv), then recalculating energies with mdrun -rerun. Such a quantity would be useless, though.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==================================================
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to