[gmx-users] solvent except water
Justin A. Lemkul
jalemkul at vt.edu
Sat Jan 16 17:25:14 CET 2010
David van der Spoel wrote:
> 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.
There are even how-to's on the Gromacs site to accomplish this:
>> 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
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
>> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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