David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 7 16:05:25 CET 2005
On Mon, 2005-03-07 at 10:44 -0400, Anthony Cruz wrote:
> How I Check compatibility with the force field I am using?
> Checking the atom types?
yes, use atom types from e.g. opls and if possible also charges.
> On Monday 07 March 2005 07:01, David van der Spoel wrote:
> > On Mon, 2005-03-07 at 06:43 -0400, Anthony Cruz wrote:
> > > Hi gmx-users:
> > >
> > > I try to simulate a protein in non aqueous solvents. I see various
> > > contributions of organic molecules in the gromacs topology section. I
> > > start to using the acetonitrile model but few days ago I found someting
> > > in the mailing list about this acetonitrile and I am not clear if the
> > > model is good or need to be corrected in some way. I will appreciate
> > > your help.
> > Start with a box of pure acetonitrile and simulate it. Check the
> > properties such as DHvap and density. Check compatibility with the force
> > field you are using before you use it for protein simulation.
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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://xray.bmc.uu.se/~spoel
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