[gmx-users] the vdw and electrostatic energy

Ran Friedman r.friedman at bioc.uzh.ch
Thu Apr 16 14:11:51 CEST 2009


This problem has been discussed for decades in the literature. There are
approaches such as PME and reaction field to deal with the long-range


Dechang Li wrote:
> Dear all, 
>      When we do a MD simulation, we always set a cutoff 
> of non-bonded interactions, e.g. r=1.2 nm. When the 
> simulation finished, we can use the command 
> g_energy -f ener.edr -s ... to abtain the non-boned 
> energy of the system. My question is whether the non-bonded 
> energy values dependent on the non-bonded cutoff? If YES,
> there may be no problem of the vdw interaction (LJ-SR), 
> because the vdw interaction vanish in a short distance. But 
> how about the electrostatic term with the distance dependence
>  of 1/r^2 ?
> Best regards,
> ========================================= 
> Dechang Li, Ph.D Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> P.R. China 
> Tel:   +86-10-62773574(O) 
> Email: lidc02 at mails.tsinghua.edu.cn
> =========================================
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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