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

[David]

On Wed, 2004-01-14 at 21:24, Yuhua Song wrote:
> 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?
> 
you can add indidividual molecules with genbox

alternatively you can grow a molecule using FEP. See recent mailing list
posts for this.
> 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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> 
> 
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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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