CCL: Solvation of organic molecules (with GROMACS)

 Sent to CCL by: David van der Spoel [spoel%x%xray.bmc.uu.se]
 Alessandro Contini alessandro.contini{}unimi.it wrote:
 
 Sent to CCL by: Alessandro Contini [alessandro.contini**unimi.it]
 Hi, you could try to use VMD/NAMD that are freely downloadable from
 http://www.ks.uiuc.edu/
 (previous registration). Moreover they can be
easily installed on all most common platforms. With NAMD it's quite easy getting started, thanks also to well done 
 tutorials, and VMD it's a powerful graphic interface. In order to work
 with organic molecules the harder part is generating the topology file,
 however you could find another nice tutorial for this at
 http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf
 Anyway, it could be harder to simulate solvents different than
 water..."black boxes" as you mean do exist, but usually are commercial
 (and quite expensive) software.
It is quite easy with gromacs too, for a molecule like benzene, and quite well described in the manual (chapter 5). For more complex molecules you can start with a topology from the prodrg server http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html which generates topologies for a number of programs and force fields, including gromacs. 
 
 Hope this help
 Alessandro
 Il giorno lun, 17/07/2006 alle 20.55 -0400, Fernando D. Vila fer#%
 #phys.washington.edu ha scritto:
 
 Sent to CCL by: "Fernando D. Vila" [fer ~~ phys.washington.edu]
 Hello everyone..
A summer student and I are trying to simulate the solvation of some organic molecules. What we want is something that is very black-box: we give it a molecule, a solvent, we choose a force field, set up some MD parameters and we running. I'm sure there is a solution "out there", it looks like a pretty easy problem. We don't need anything very sophisticated since we are just trying to generate some MD snapshots to use in explicit solvent ab initio calculations of UV-Vis spectra (we just want to check a couple of ideas).
He downloaded GROMACS and got it running. The problem he run into is that, although it is very easy to generate inputs for solvated ions and solvated polypeptides, it isn't very clear how to generate them for an arbitrary organic molecule like, say, benzene or aniline.
I'm willing to drop GROMACS if anyone thinks there is an easier solution. 
   Any suggestions will be quite welcome.
 Best regards, Fer.
 Ubi dubium ibi libertas.
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 Fernando D. Vila                Voice    (206)543-9697
 Department of Physics           Fax      (206)685-0635
 University of Washington        E-mail   fdv[A]u.washington.edu
 Seattle, WA 98195, USA          WWW      http://faculty.washington.edu/fdv
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 --
 David.
 ________________________________________________________________________
 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=-=xray.bmc.uu.se	spoel=-=gromacs.org   http://folding.bmc.uu.se
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