Re: Running CGMD using NAMD

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jul 29 2008 - 11:39:54 CDT

Hi Anirban,
this depends on what CG model you want to use, as the interface in vmd
is rather general and is designed to let you use several different
coarse graining methods. I can send you topology/parameter files if it
is a standard model we have used in the past. If you're doing
shape-based coarse graining, you need to develop parameters for your
system as described in the relevant papers.
Best,
Peter

Anirban Ghosh wrote:
> Hi All,
>
> I want to perform CGMD using NAMD. I ahve built the CG model of my protein
> using VMD. How should I use NAMD now to do the simulation? Is there any
> specialized force field in NAMD to be used for CGMD? Or else how should I
> built the required force field for CGMD.
>
> Thanks a lot.
>
> Regards,
>
>
>

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