[gmx-users] acetonitrile

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 7 12:01:01 CET 2005

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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