[gmx-users] Calculate interaction energy dynamically

[Justin Lemkul]

On 7/23/13 11:05 AM, Davit Hakobyan wrote:
> 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?
>

Where do they come from - mdrun? g_energy? gmxcheck?  If you haven't run 
gmxcheck on the .edr file, please do.

>>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?
>

Yes.  There are several intramolecular terms that can come into play here.

> 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?
>

Upon what do you base your feeling?  In principle, this is a very simple 
calculation to decompose the short-range nonbonded interactions in a pairwise 
fashion.  Note that these are not free energies and there is no reason to 
believe that any given force field will be able to produce a physically 
meaningful value here as the force field almost certainly wasn't parameterized 
to reproduce such a value.

-Justin

-- 
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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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