[gmx-users] Calculating area per lipid and monolayer thickness

[Merril Mathew]

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
>> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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