[gmx-users] solvent except water
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jan 16 13:44:22 CET 2010
rasoul nasiri wrote:
> I want to use a solvent with two types molecules (for example linear and
> cyclic Glucose form).
> How can I fill box with them?
You can use genbox with mixed solvents.
> I highly appreciate for advice given me!
> Best Regards
> On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
> leila karami wrote:
> Dear David
> in genbox command system solvated by water molecule by default.
> but I want solvent except water.
> leila karami
> OK, now I understand.
> You can give to genbox any solvent that you like, provided that each
> molecule consists of a single residue (the residue number is used to
> distinguish molecules). In the gromacs distribution there are a
> couple of other solvents present. Look in share/gromacs/top
> directory of your installation (or roll your own).
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> spoel at gromacs.org <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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