Re: Force field for coarse grained simulations (and other questions)

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jul 12 2007 - 07:58:12 CDT

Hi Patrick,
the paper you're referring to would be set up using shape-based, not
residue-based, coarse graining. If you let me know which one you're
referring to, I can give you more details about obtaining a forcefield
off-list (for shape-based CG, the parameters will need to be derived for
your system, using the procedure given in that paper and in /Biophysical
Journal/, 91:4589-4597, 2006).

For residue-based CG, you'd want to use the same parameters as in
Marrink's papers (since they are the basis for that model). For
shape-based CG, it's going to depend on your system; you need to choose
a value that's some small multiple (2-3) of the average rmin for your
nonbonded interactions. Values on the lower end of that range are
appropriate if you're mostly simulating the interactions of subunits in
a well defined structure; you may need the higher end if you want to see
aggregation. (which we haven't yet tried using this model -- some
refinements are probably needed).

The config files really are identical to a normal config file except for
the changes in timestep, nonbonded cutoff, and such. Again, I can send a
copy if you like, but I need to know what kind of simulation you're
planning first.

Best,
Peter

patrick wintrode wrote:
> Hi.
>
> I want to set up a CG simulation using the residue based coarse
> graining tools that are included in the latest version of VMD.
>
> In the paper I read (the virus simulation by Arkhipov in Structure,
> 2006) it said that a "CHARMM style force field" was used. Does anyone
> have more details on this, or know where it can be obtained?
>
> Also, is there a common choice for cutoff distances and timesteps for
> residue based CG simulations, or do the need to be chosen on a case by
> case basis?
>
> Finally, does someone have a sample .conf file for CG simulations
> (like the samples available for standard NAMD simulations)?
>
> Thanks.
>
> Patrick L. Wintrode
> Assistant Professor
> Dept. of Physiology & Biophysics
> Case Western Reserve University
> Cleveland, Ohio 44106

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