[gmx-users] Calculate interaction energy dynamically

[Davit Hakobyan]

Thank you very much for your continuous support.

> Date: Tue, 23 Jul 2013 12:06:57 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
> 
> 
> 
> 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.
> 

The above warnings are issued by mdrun. The g_energy generates similar warnings like:

WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=74000.
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=75000.
Trying to skip frame expect a crash though
Last energy frame read 75 time 75000.000
...

The gmxcheck command:

gmxcheck -f system_ordered.trr -c system_ordered.tpr -n system_ordered.ndx -e system_ordered.edr

does not give any warning/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?
> >
> 
> 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.

You should be right concerning the vdw values since my feeling was mistakenly based on resembling these absolute values with the difference of the interaction energies between the final and initial configuration (which is ~15-20 kJ/mol).

Please let me know if you would have a suggestion about the above mdrun/g_energy warnings.

Thanks very much again for your help and time.

> 
> -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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