[gmx-users] Calculating area per lipid and monolayer thickness
jalemkul at vt.edu
Wed Mar 8 13:56:54 CET 2017
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?
> and which option should I choose from the list?
The ones I said before, (the aptly named) Box-X and Box-Y.
> 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
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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
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