[gmx-users] Re:Re: the vdw and electrostatic energy (Ran Friedman)

Dechang Li li.dc06 at gmail.com
Thu Apr 16 18:15:43 CEST 2009

>Message: 3
>Date: Thu, 16 Apr 2009 14:11:51 +0200
>From: Ran Friedman <r.friedman at bioc.uzh.ch>
>Subject: Re: [gmx-users] the vdw and electrostatic energy
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <49E72087.8020203 at bioc.uzh.ch>
>Content-Type: text/plain; charset=GB2312
>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
	I did not mean that. I want to know that when we use g_energy in Gromacs to 
read the energy from the file ener.edr, does the cutoff affect the values
of the energy? For example, when the cutoff is set to 1.2 nm and the PME method
is used, does the energy term "Coul-SR" read by g_energy contain the long range
part ?

>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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