Re: all-atom to coarse-grained system

From: Victor Kwan (
Date: Fri Feb 02 2018 - 14:03:39 CST

Hi Rebeta,

Before doing anything, think about how you define 'better'.


Victor Kwan

On 2/1/2018 4:29 PM, Rabeta Yeasmin wrote:
> Dear NAMD users,
> I am trying to convert my all-atom umbrella sampling system containing
> protein-lipid-water-ions into a coarse-grained system. I have already
> prepared windows at different distances and equilibrated them using
> all-atom simulation. I am wondering if I can continue the simulation
> from there converting them into a coarse-grained system or I have to
> start building system from the beginning.
> I have seen two methods for converting all-atom simulation to
> coarse-grained simulation in VMD CG tools plugin--residue based
> coarse-graining (rbcg) and shape based coarse-graining (sbcg). I am
> wondering which one will be better for my system.
> I have tried in rbcg method, it has two .cgc files which convert
> protein and water into the coarse-grained system. I am wondering how
> can I find cgc file for lipid and other ions.
> Thanks.
> Rabeta Yeasmin

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