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.
