[gmx-users] How to add small molecule in the solvent?

[David]

On Wed, 2004-01-14 at 20:58, Yuhua Song wrote:
> Hi, everyone:
> 
> I need to add some small molecules into the solvent. When I add the mono
> atomic ions: we can just use the "genion". Now I want to add some small
> molecules into the solvent just as I add the mono atom ions to randomly
> distributed in the solvent. How could I do implemented this?
> 
Easiest is to start with genconf (assuming you have your small molecule
ready), you multiply the small molecule conformation. Then use genbox to
solvate and mdrun with pressure coupling.


> Thank you very much in advance,
> 
> Yuhua
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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