From owner-chemistry@ccl.net Fri May 14 10:48:01 2010
From: "qing shao shaoqingfly1981++gmail.com" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: simulation
Message-Id: <-41851-100512214303-27143-KiRb8PxADjxAu2tfYFhrxw.:.server.ccl.net>
X-Original-From: qing shao <shaoqingfly1981]~[gmail.com>
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Date: Wed, 12 May 2010 17:40:19 -0700
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Sent to CCL by: qing shao [shaoqingfly1981^-^gmail.com]

Ramya
  I think you can try "editconf" to put your solute in the center of
your box and "genbox" to generate your solvents. Please read the
manual for more information.
Regards
Qing

On Wed, May 12, 2010 at 2:57 AM, rinu iyer rinuiyer{:}gmail.com
<owner-chemistry%ccl.net> wrote:
> dear subscribers,
> =A0=A0=A0=A0=A0=A0=A0=A0 i am using gromacs . i want to run a calculation=
 in which i want to
> place a molecule in the centre during the generation of the box to do
> molecular dynamics simulation. the molecule is surrounded by solvents.
> can u tell me please how to run this calculation.
>
> Thanks in advance
> K.R.Ramya
> research fellow
> Indian Institute of science,Pune
> Tower, Sai Trinity Building, Sutarwadi Road, Pashan,
> Pune 411021, INDIA
>