all-atom to coarse-grained system

From: Rabeta Yeasmin (
Date: Thu Feb 01 2018 - 15:29:45 CST

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.


Rabeta Yeasmin

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