[gmx-users] MD with bilayer

[Itamar Kass]

Hi,

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.

Cheers,
Itamar

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
>
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