[gmx-users] [Fwd: question]

David van der Spoel spoel at xray.bmc.uu.se
Tue Jul 29 19:54:45 CEST 2008

-------- Original Message --------
Subject: question
Date: Tue, 29 Jul 2008 16:57:39 +0200 (CEST)
From: Morteza Khabiri <khabiri at greentech.cz>
To: spoel at xray.bmc.uu.se

Dear Dr.David van der Spoel

I am quite unexperienced user of gromacs and unfortunately I have to
create my own solvent box for formamid and some other organic solvent.
Actually maybe I could find some other group which work on this solvent
before but I am strongly interested to learn how could I creat organic or
other solvent box and also forcefield files by myself. Would you please be
so kind and briefly tell me how to do it?

Check literature for an appropriate force field (OPLS might work) and 
read chapter 5 of the manual. Please ask further questions on the 
mailing list.

Thank you very much in advance


Ph.D student of Biophysics
Laboratory of High performance computing
Institute of Systems Biology and Ecology ASCR
Institute of Physical Biology,
University of South Bohemia
Zamek 136 373 33, Nove Hrady
Czech Republic
Email: Khabiri at greentech.cz
mobile: +420 773 903 109

David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se

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