[gmx-users] Calculating area per lipid and monolayer thickness
mmathe01 at mail.bbk.ac.uk
Wed Mar 8 13:52:11 CET 2017
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" <jalemkul at 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
>> 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
>> than the initial configuration file. So does the box X and Y get smaller
> 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 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
> jalemkul at 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-request at gromacs.org.
More information about the gromacs.org_gmx-users