On 12/26/13, 5:30 AM, lloyd riggs wrote:
Zero it--> If you plot a potential energy value strait from the simulation it will be something like point a) -7000 point b) -7050 across a single simulation. Thus you have to find a beginning point and subtract it across the run. Additionally, fluctuations may dictate 10 or so runs to determine a good mean, as the drifet or error might be 20 kcal/mol in a system. As I read your other post, I would assume the experiment would be non random placement of DMSO in water (say a wall system), otherwise you would be looking at a single molecules energy dictated by conformational space over time...ie something like Justin's post...which you still may have to calculate a mean for, but I assume this is done through the -nmol option. You still also may have to "zero it", but I am not sure, direct use of g_energy gives abitrary starting points as above from my experience.
The values printed by g_energy are not arbitrary. They are the energy of a mole of equivalent systems of a given configuration, hence their large magnitude.
-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.