On 3/8/17 7:28 AM, Merril Mathew wrote:
I have a system that I simulated using GROMACS v5.0.4. The system is two monolayers of lipid on each side of a box of water. I would like to know if there is a way to calculate area per lipid and monolayer thickness. I read that one can use gmx energy to find box size in X and Y and you divide the average time evolution box size( X*Y) by number of lipids. I used commmand: gmx energy -f md.edr -s md.tpr -o box_vector.xvg What option should I select when prompted to get X and Y box dimensions.? How is the box vector calculated? I have noticed that the lipids pack closely after simulation, that means the the area per lipid will be smaller than the initial configuration file. So does the box X and Y get smaller as well?
What you want are Box-X and Box-Y from the .edr file. Then you can see the time series of how the box size changes.
-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.