[gmx-users] MD with bilayer

Itamar Kass itamar.kass at gmail.com
Mon Nov 9 22:15:07 CET 2009


VMD was built to work with NAMD, so the atom names and topologies will not
work with GROMACS. I guess you better go to Peter Tieleman site (
http://moose.bio.ucalgary.ca/) and rad there how to do things.


On Tue, Nov 10, 2009 at 8:05 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> parthiban at ncbs.res.in wrote:
>> Hi
>> I have constructed the bilayer with protein molecule in VMD.
>> Can any one tell how to start MD from here.
> Follow the methods of whichever tutorial you learned from :-)
>  the initial step - pdb2gmx is not working for this complex(pdb+membrane)
> We're not omniscient... tell us what you did, what you expected, what you
> saw and why you think it was not working :-)
> Mark
> --
> gmx-users mailing list    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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091110/2a0f9ee5/attachment.html>

More information about the gromacs.org_gmx-users mailing list