From owner-chemistry@ccl.net Fri May 14 12:32:00 2010
From: "Soren Eustis soreneustis!A!gmail.com" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL: simulation
Message-Id: <-41854-100514114755-26520-Sf5etctm5DtqfDYHOQItUQ a server.ccl.net>
X-Original-From: Soren Eustis <soreneustis#gmail.com>
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Date: Fri, 14 May 2010 17:47:38 +0200
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Sent to CCL by: Soren Eustis [soreneustis]*[gmail.com]
Ramya,

   In addition, Packmol works very well for this.  It can be downloaded at:
http://www.ime.unicamp.br/~martinez/packmol/.

Soren


--=20
Dr. Soren N. Eustis
ETH =AD Zurich
Institute for Biogeochemistry and Pollutant Dynamics
Universitatstrasse 16
8092 Zurich

+41 44 632 93 48 (office)
+41 44 632 14 38 (fax)

soren:env.ethz.ch


On 5/13/10 2:40 AM, "qing shao shaoqingfly1981++gmail.com"
<owner-chemistry:ccl.net> wrote:

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> Sent to CCL by: qing shao [shaoqingfly1981^-^gmail.com]
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> 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
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> On Wed, May 12, 2010 at 2:57 AM, rinu iyer rinuiyer{:}gmail.com
> <owner-chemistry*o*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 wan=
t 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.
>>=20
>> Thanks in advance
>> K.R.Ramya
>> research fellow
>> Indian Institute of science,Pune
>> Tower, Sai Trinity Building, Sutarwadi Road, Pashan,
>> Pune 411021, INDIA
>>=20
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> -=3D This is automatically added to each message by the mailing script =3D->=20>=20>=20>=20>=20>=20>=20>=20>=20
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