On 10/16/14 11:42 AM, James Lord wrote:
Hi Justin, Sorry for not being clear, I have done the simulation without specifying the energygrps, so based on your previous comment I should use mdrun -rerun trj.xtc -o energy.edr -pn index.ndx? and in index file define energygrps = Protein Surface right? If not appreciate if you give an example of the command with appropriate input output etc.
Create a new .tpr with the .mdp file that specifies the desired energygrps, then: mdrun -s new.tpr -rerun trj.xtc -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
