VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 31 2011 - 21:44:25 CDT

Hi Sibel,
I've just committed a vastly improved version of the reverse coarse
graining function to the vmd cvs, which will do rotations of the
bead-defined groups to give a much better structure than you get using
the current version. If you get the cvs version of vmd, you can just do
reversal with rotations enabled (there will be a gui option) to get
cleaner results. You should still anneal the structure, and check the
resulting chirality, but in my experience this gives you a much more
reasonable starting structure.
Best,
Peter

On 03/31/2011 12:10 PM, Peter Freddolino wrote:
> 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
>>