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

[Justin Lemkul]

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" <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
>>
>> ==================================================
>> --
>> 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.
>>

-- 
==================================================

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

==================================================