VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 31 2011 - 21:46:14 CDT

Hi Vlad,
Thanks for the suggestion. I tried to make the cgtools plugin as general
as possible --that's why it makes use of user-definable database files
in what I hope is a pretty simple format, so that a wide variety of
models can be used with it. That also means that having tools for
various approaches to reverse coarse graining would be great. I'm not at
TCBG any more and don't have time to do active development, but if you
already have a tool, you might want to speak with Kirby Vandivort
(kvandivo_at_ks) to see if it can be integrated with cgtools as another
option for reverse coarse graining. You'll probably need to make it work
with the cgtools bead definition and reverse coarse graining database
formats, but these are *really* simple.

Best,
Peter

On 03/31/2011 01:39 PM, Vlad Cojocaru wrote:
> Dear Peter, Dear VMD users,
>
> I do not have experience with coarse graining in VMD+NAMD, I used
> GROMACS mainly.
> However, I developed a coarse grain to all atom conversion for the POPC
> membranes and which I wrote for VMD. The procedure is compatible with
> the AMBER (gaff) force field currently and is submitted for publication.
> The extension to CHARMM and other force fields is relatively straight
> forward.
>
> A similar approach to the one I took was recently published for Gromacs:
> This approach is general both for proteins and lipids.
>
> Stansfeld, P.J., and Sansom, M.S.P. (2011). From coarse grained to
> atomistic: a serial multiscale approach to membrane protein simulations.
> J. Chem. Theory Comput., in press
>
> My procedure currently works only for POPC, it works with VMD and AMBER
> (but it can be easily adapted to work with VMD and NAMD) and achieves an
> rmsd of 1 -1.5 between the CG and AA lipids. If there is interest in
> it, I could provide the files to the VMD/NAMD community as soon as our
> paper will be accepted..
>
> Then, it can be further developed to include the entire procedure
> described by the article above ... Include other lipids, proteins and so
> on ...
>
> Best wishes
> Vlad
>
>
> On 03/31/2011 06:10 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
>>>
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cellular and Developmental Biology
> Roentgenstrasse 20
> 48149 Muenster, Germany
> tel: +49-251-70365-324
> fax: +49-251-70365-399
> email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>