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

David spoel at xray.bmc.uu.se
Wed Jan 14 21:17:01 CET 2004

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 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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