VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 31 2011 - 11:10:35 CDT

Dear Sibel:
>From the very fine manual:

""" The coarse grained molecule that you wish to convert back to
all-atom needs to be loaded in VMD and selected as the Coarse-Grained
Molecule. In addition, CG Builder needs to have the original all-atom
molecule available and loaded into VMD. Select this molecule as the
All-Atom Molecule. You will need to specify the work file that was saved
in the earlier step as the Rev CG File. And, the reconstructed all-atom
representation molecule will be saved as PDB file with the given name.

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. """

Coarse graining involves information loss, so you cannot expect to get
out a perfect all-atom structure at the end. CGtools handles this by
having you do simulated annealing on the atomistic structure with
restraints in place such that you sample the region of all-atom
conformational space consistent with the cg coordinates at the time of
reverse coarse graining.

I did have some new code checked in that should at least make optimal
use of the information that *is* available in the cg structure by
preserving orientations of groups relative to each other, but I need to
check whether that is enabled or needs a secret magic switch. I'll post
on that later today.

Best,
Peter

On 03/30/2011 08:39 AM, Sibel Cakan wrote:
>
> Dear all
> I have performed a CG MD simulation of a protein which is embedded in a
> membrane.Now I am trying to reverse coarse-grained into all atom
> structure using the CG Tools plugin in VMD 1.8.7 for comparing CG
> simulation results with all-atom simulation.
> But the reversed structure have some unusual bonds (like a
> triangle,etc.) .I tried to reverse initial CG structure before MD was
> done and this worked there are not unusual bonds or anything else.
> Any suggestion would be appreciated.
> Thank you
> Sibel
>