[gmx-users] Re: dmf or dmso

[David van der Spoel]

On Tue, 2003-05-13 at 11:46, jiri vondrasek wrote:
> Hello David
> I noticed you have helped to someone who needed solvent box of different
> molecule than water. Are you aware of an existence or did you create by
> yourself a solvent box of N,N-dimethylformamide or dimethylsulfamide? I
> would appreciate any kind of advice how to get them.
> Thank you
First of all you need a force field for the molecule.

Then I would recommend building the molecule in a program like molden,
and minimize the single molecule in gromacs using your
parameters, charges etc. Then you build a box using e.g. genconf and
simulate it with pressure coupling until it the
density and potential energy equilibrate.

>  
> jiri
>  
> Dr Jiri Vondrasek
> Institute of Organic Chemistry and Biochemistry 
> and 
> Center for Complex Molecular Systems and Biomolecules   
> Flemingovo namesti 2, 166 10 Prague 6
> Czech Republic
> tel:420-220 183 257
> fax:420-220 183 292
> e-mail:jiri.vondrasek at uochb.cas.cz
>  
> 
> ---
> Odchozi zprava neobsahuje viry.
> Zkontrolovano antivirovym systemem AVG (http://www.grisoft.cz).
> Verze: 6.0.476 / Virova baze: 273 - datum vydani: 4/24/2003
>  
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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