David van der Spoel wrote:
rasoul nasiri wrote:
Hi
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.
There are even how-to's on the Gromacs site to accomplish this:
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
-Justin
I highly appreciate for advice given me!
Best Regards
Rasoul
On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@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.
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
sp...@gromacs.org <mailto:sp...@gromacs.org> http://folding.bmc.uu.se
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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