Re: Broken Structure after reverting coarse-grained system to all-atom system

From: Peter Freddolino (
Date: Tue Jul 10 2018 - 09:07:44 CDT

Can you please elaborate on what you mean by "broken"? The way that namd
does reverse CG should give structures that have atoms in roughly the right
places, but the orientations will not be perfect, and some relaxation will
be required. Quoting the cgtools documentation:
"A simulated annealing run from NAMD will usually need to be run after
reconstruction of the all-atom model. The annealing run needs to be run in
a specific way, so the CG builder tool can create the proper NAMD
configuration files to use. By default the CHARMM parameter file (used by
several other VMD plugins) will be used for the config file, but you can
alter this as desired. In addition, the PSF filename will be needed for the
NAMD simulation."

The config file generated by cgtools should have appropriate constraints to
run the needed refinement.

On Mon, Jul 9, 2018 at 1:38 PM, Rabeta Yeasmin <>

> Hi,
> I have a protein-lipid system that I converted to a coarse-grained system
> using residue-based coarse-graining method and run Steered MD and
> umbrella sampling. After running around 350ns, I have reverted the last
> structure of all windows to the all-atom system using the
> reverse-residue-based coarse-gaining method. But I found the protein and
> lipid structure are broken in the all-atom system. Is that am a usual
> thing?
> Thanks.
> Rabeta Yeasmin

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