[gmx-users] Re: electrostatic and vdw energies from snapshots

Mauricio Pablo Sica msica at unq.edu.ar
Thu Apr 5 15:21:08 CEST 2007

Maybe it is an obvious observation, but reruns are not as time consuming 
as original runs. If I'm not wrong, as snapshots are generally saved 
every 2500-10000 time-steps, reruns are 2500-10000 faster than original 

So, maybe a simple rerun with new 'energygrps' is your option.

Additionally, I don’t think that minimized snapshots are very 
representative of the energy of a run. 


> On 4/5/07, merc mertens <merc.mertens at gmx.net> wrote:
> > hello,
> >
> > i would like to calculate the vdw and electrostatic energies for a
> part of my system that was not included in the energy groups during md.
> as a rerun would be too time consuming, i thought of taking snapshots
> from the md run, minimising those with the part of interest included in
> the energy groups. then one could calculate estat and vdw energies from
> the energy file from the minimisation. is this to simply thought??
> >
> > merc

Dr. Mauricio P. Sica                    LEPP
Phone: (54011)4365-7100 ext. 169        Laboratorio de Expresión
R. Saenz Peña 354                       y Plegado Proteico
(B1876BXF) Bernal, Buenos Aires         Universidad de Quilmes

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