I am not sure what command to use to extract the X and Y box vector. is it gmx energy -f md.edr -o .xvg? and which option should I choose from the list?
On 8 Mar 2017 12:44 p.m., "Justin Lemkul" <jalem...@vt.edu> wrote: > > > 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. > -- 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.