[gmx-users] water-vacuum-water simulation

[luisa pugliese]

thank you very much for the message. However I don't understand how can I 
tell the program where in the box I want water to stay and where is vacuum. 
Can you please explain me in a more explicit way how to set up the system. 
Then, once I have set up the box with water on the outer part and vacuum in 
the middle, which force field do you think it would be better to use?
Best regards
Luisa
=============================
Luisa Pugliese, Ph.D.
luisa.pugliese at safan-bioinformatics.it
S.A.F.AN. BIOINFORMATICS
Corso Tazzoli 215/13 -10137 Torino - ITALY
tel +39 011 3026230
fax +39 011 3165080
cell. +39 333 6130644

----- Original Message ----- 
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, October 25, 2006 9:08 AM
Subject: Re: [gmx-users] water-vacuum-water simulation


> luisa pugliese wrote:
>> Dear all,
>>   I would like to perform a molecular dinamics simulation of a GPCR in a
>> water-vacuum-water box system. Anybody knows if it is possible to do it 
>> with
>> GROMACS and what should I do?
>> Thank you to all
>> Luisa
>> =============================
>> Luisa Pugliese, Ph.D.
>> luisa.pugliese at safan-bioinformatics.it
>> S.A.F.AN. BIOINFORMATICS
>> Corso Tazzoli 215/13 -10137 Torino - ITALY
>> tel +39 011 3026230
>> fax +39 011 3165080
>> cell. +39 333 6130644
>>
>>
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> just extend the box length in one dimension.
>
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://folding.bmc.uu.se
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