[gmx-users] Calculate interaction energy dynamically

[Davit Hakobyan]

Thanks very much for all your suggestions!

> One way that you might approach it is to use mdrun -rerun.  You could order the 
> lipids with respect to the lipid of interest, such that the reference lipid is 
> always molecule N and the nearest lipid is always written as N+1 in the ordered 
> trajectory file.  Then use normal index groups as your energygrps in the .mdp 
> file and recalculate the energies with mdrun -rerun.

Do I understand correctly that in the ordered trajectory each frame should have lipids ordered is such a way that in any two frames N and M the lipids with n and n + 1 indices should be neighbors but these need not necessarily be the same lipids in two frames ?

Could you also please inform what command may one use to reorder lipids in a trajectory per frame?

Thanks very much for all the help.

> Date: Mon, 22 Jul 2013 08:04:27 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
> 
> 
> 
> On 7/22/13 6:20 AM, Davit Hakobyan wrote:
> > Dear Gromacs Users,
> >
> > Is there a way in Gromacs to calculate the interaction energy between any two neighbor lipids dynamically? Since the neighbor lipids change over time in the trajectory file specifying a static energy groups in the input script will not help.
> >
> > Is there a way to accomplish this?
> >
> > One could use the g_select tool to define dynamic groups but again the energy file needs a predefined groups which probably makes the g_select tool useless in this case?
> >
> 
> One way that you might approach it is to use mdrun -rerun.  You could order the 
> lipids with respect to the lipid of interest, such that the reference lipid is 
> always molecule N and the nearest lipid is always written as N+1 in the ordered 
> trajectory file.  Then use normal index groups as your energygrps in the .mdp 
> file and recalculate the energies with mdrun -rerun.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> 
> ==================================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists