[gmx-users] solvent except water

rasoul nasiri nasiri1355 at gmail.com
Sat Jan 16 11:51:11 CET 2010


I want to use a solvent with two types molecules (for example linear and
cyclic Glucose form).
How can I fill box with them?

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>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    spoel at gromacs.org   http://folding.bmc.uu.se
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