[gmx-users] question regarding genion

Vigneshwar Ramakrishnan vmsrvignesh at gmail.com
Fri Sep 12 10:54:50 CEST 2008

Hi Sarbani,

I think you should use "genion -random no" along with other options.


On Fri, Sep 12, 2008 at 3:30 PM, sarbani chattopadhyay <
sarbani_c84 at rediffmail.com> wrote:

>   Hi everybody,
>                       I want to place my counterions close to the charged
> amino acids. I am aware of
> the fact that even if the counterions are randomly added yet they will
> eventually settle during
> equlibration. But still I will like to start with a structure that has
> counterions close to charged
> residues.
> I have been going through the archive and the manual but I could not figure
> out how to
> disable the default option of "-random" while using the "genion" command.
> Can anyone guide me through the command that is required to add counterions
> based on
> potential so that the counterions are closed to the charged residues?
> Thanks  in advance
> Sarbani
>   [image: Ebay]<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,

"Strive for Excellence, Never be satisfied with the second Best!!"

"The rewards of sincere resolves are highs money can never buy!"
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080912/e925822a/attachment.html>

More information about the gromacs.org_gmx-users mailing list