.
Sincerely:
YeQing
--- 09年11月29日，周日, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] An unexpected behavior of rdf calculated by the g_rdf
command
收件人: "Discussion list for GROMACS users"
日期: 2009年11月29日,周日,上午10:57
青 叶 wro
7日，周五, Lukasz Cwiklik 写道operation：
发件人: Lukasz Cwiklik
主题: Re: [gmx-users] An unexpected behavior of rdf calculated by the g_rdf
command
收件人: "Discussion list for GROMACS users"
日期: 2009年11月27日,周五,下午10:06
On Fri, Nov 27, 2009 at 6:40 AM, 青 叶 wrote:
>
> Hello all gmx-users:
>
Hello all gmx-users:
I have run a 100ns long MD simulation, the system is HAuCl4 acid
solution, which contains one [AuCl4]- cluster and 503 water moleculars, and
calculated the rdf by using the g_rdf command as follow:
g_rdf -f yqqmd.trr -s yqqmd.tpr -n yqq.ndx -o rdf.xvg -cn cn.xvg -rdf a
I did a energy minimization on a system contain one [AuCl4]- and 503 water
moleculars, by using a self-define non-bond interaction (which is obtain from
ab-initio calculation), my em.mdp file is as follow:
title = yqq
cpp = /usr/bin/cpp ; the c pre-processor
de
Hello everybody:
I have read GROMACS' manual and found that the non-bond interaction in
GROAMCS is describled as Coulomb term add A/r^12 -B/r^6 which is named
Lennard-Jones term, but recently I have read some papers which use a
effective-two-body potential to describle the non-bond intera
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