[gmx-users] solvent except water

[Justin A. Lemkul]

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 
>> <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
>>     --     gmx-users mailing list    gmx-users at gromacs.org
>>     <mailto:gmx-users at gromacs.org>
>>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>>     Please search the archive at http://www.gromacs.org/search before
>>     posting!
>>     Please don't post (un)subscribe requests to the list. Use the www
>>     interface or send it to gmx-users-request at gromacs.org
>>     <mailto:gmx-users-request at gromacs.org>.
>>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
> 
> 

-- 
========================================

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

========================================