[gmx-users] Calculate interaction energy dynamically

[Davit Hakobyan]

Thanks so much for the suggestion.

By using the command:

trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr

the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm).

Then by specifying new energy groups like lipid1, lipid2, etc the energy file was generated with the "rerun" flag:

mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o system_ordered_useless.trr  -c system_ordered.gro  -e system_ordered.edr

many warnings were shown like:

WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=31000.
Trying to skip frame expect a crash though

WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=32000.
Trying to skip frame expect a crash though

WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=33000.
Trying to skip frame expect a crash though

Do these warnings point to some error? 

>From the generated energy file one optionally could select not only coulomb and vdw terms between the goups lipid1, lipid2 and lipid3 but also between lipid1 and lipid1. The coulomb output of lipid1-lipid1 is 0 while vdw is ~ -30-40 kJ/mol. Since the latter is the vdw energy of a lipid with itself should one understand this value as the interaction between different atoms of one lipid?

The vdw interactions between lipid1-lipid2 is also ~ -30-40 kJ/mol. Apart from the feeling that these vdw numbers are ~ twice larger than they should does this procedure contain some obvious problems?

Thanks very much for all the help.

> Date: Mon, 22 Jul 2013 08:39:27 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
> 
> 
> 
> On 7/22/13 8:37 AM, Davit Hakobyan wrote:
> > 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 ?
> >
> 
> Yes.
> 
> > Could you also please inform what command may one use to reorder lipids in a trajectory per frame?
> >
> 
> Start by reading trjorder -h.  The exact approach depends on what you're dealing 
> with.
> 
> -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
> 
> ==================================================
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