I dont know what I am doing wrong. There is no Box-X or Box-Y when prompted. These are the list I get: ----------------------------------------------------------------- 1 Angle 2 Proper-Dih. 3 Ryckaert-Bell. 4 Improper-Dih. 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Disper.-corr. 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Conserved-En. 15 Temperature 16 Pres.-DC 17 Pressure 18 Constr.-rmsd 19 Vir-XX 20 Vir-XY 21 Vir-XZ 22 Vir-YX 23 Vir-YY 24 Vir-YZ 25 Vir-ZX 26 Vir-ZY 27 Vir-ZZ 28 Pres-XX 29 Pres-XY 30 Pres-XZ 31 Pres-YX 32 Pres-YY 33 Pres-YZ 34 Pres-ZX 35 Pres-ZY 36 Pres-ZZ 37 #Surf*SurfTen 38 T-DPOPG_OPO 39 T-SOL_Ion
38 and 39 are the coupling groups I used. Merril. On 8 March 2017 at 12:56, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/8/17 7:52 AM, Merril Mathew wrote: > >> 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? >> > > Yes. > > and which option should I choose from the list? >> >> > The ones I said before, (the aptly named) Box-X and Box-Y. > > -Justin > > > 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. >>> >>> > -- > ================================================== > > 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.