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

[Yuhua Song]

The situation is that I have a equilibrated systems of biomembrane in a box
of water and the ions in the solvent. Now, I want to add some small
molecules into this equilibrated system of solvent. In this situation, what
should I do?

Thanks,

Yuhua



> > 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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