[gmx-users] crude interaction energy using g_energy

lloyd riggs lloyd.riggs at gmx.ch
Mon May 28 12:44:22 CEST 2012

I think the reality of biological systems is represented as such accurately.  Everyone always strives in biochemistry for a precise number, ie binding affinity = 489.489 exactly.  In real systems there are to many variables (solvent, ions, particular position of moving amino acids at point A or B, etc...).  The original rule of thumb for beginning to study these systems was to do >100 MD simulations, but I personally think a small sample space will give you the same exact mean and STD deviation, STD error, etc... (ie 10-20 runs).  There is, as larger MD's are now becoming more common still no set standard for this.

A quick way, which also generates the same variability but is faster (if you dont want a nice curve and just the end mean value) is to do MD A at the bound position and EQ it for a couple nano seconds using NV P and T, and then state B unbound the same, then 20 runs is manageable time wise, but you get no pretty curves, ie no transition states which are of interest in many cases, such as particular amino acids, or conformational changes which include several states.

I think this might help, although some analysis tools for large scale biological systems (ie say pulling contributions energy wise for a particular amino acid) would be an asset...as I have found none that dont require pulling energies, etc...alot of work at the moment.

Stephan Watkins
Univerity of Bern

-------- Original-Nachricht --------
> Datum: Sun, 27 May 2012 20:44:48 -0400
> Von: "Justin A. Lemkul" <jalemkul at vt.edu>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] crude interaction energy using g_energy

> On 5/27/12 8:41 PM, sai nitin wrote:
> > Dear all,
> >
> > Recently i performed  two 15ns simulation of  protein-ligand systems
> using
> > gromacs of my interest...and using g_energy tool..i calculated crude
> > interaction energy based on short-­‐range energy components Eint =
> <ELJ> +
> > <ECoul>. ...I got two Eints for two simulations
> >
> > 1) Eint = -51.003 Kcal/mol (first simulation)
> > 2) Eint = -26.615 Kcal/mol (second simulation)
> >
> > Can anybody tell me what meaning can i make out of it...means is first
> > simulation is more stable than second one..or vice versa...
> >
> I don't think you can say anything about stability based on these figures.
>  In 
> simulation 1, the interaction is more stable than in simulation 2.  It
> seems 
> clear that the two simulations behaved somewhat differently, but the exact
> differences will only become apparent through other analyses and
> visualization.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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