Re: vmd-l: Re: Fwd: conf file for coarse grained simulation

From: Axel Kohlmeyer (
Date: Tue Dec 15 2009 - 11:16:14 CST

On Tue, 2009-12-15 at 17:01 +0100, Francesco Pietra wrote:
> I forgot to ask: could you please suggest how roughly modify the
> parameters for cg solvation? I must have misinterpreted the analysis
> of inter-cell gap. In particular, the relationship between "Boundary"
> and "Box padding" is not clear to me.

please have a look at the online help of the solvate command. the
html file is a bit terse in that respect and should be updated.
also the URL pointing to the namd tutorial is off by one node...

the boundary value is the distance between the solvent and solute.
the default value of 2.4 is fairly generous, but due to the increased
size of water (Martini rolls 4 waters into one site) and protein
side chain "atoms", stepping this up to, say, 4.0 might be a safe
choice. this can be easily rationalized from applying common sense:
just compare the values in an all-atom .par file to the coarse grain
.par file. the r2min/2 value in the CG .par file is 2.35 whereas the
corresponding AA values are between 1.3 and 1.8 with a few around 2.0.

since your system was minimizing fine w/o periodicity, the default
might already be mostly ok for you. these values are empirical anyways.

the padding value is how much solvent outside of min/max dimensions
of the solute you want to add. so, dimensions of solute _plus_
padding dimensions will be the new min/max of your system. AFAIK,
this does not include a "safety" (i.e. the equivalent of boundary for
inter cell distance), so i would just add that value or more to your
box dimensions.

when visually checking for overlaps with PBC, you have to increase
the diameter of your vdw spheres (i just double them for our CMM
cg model).


> thanks
> francesco

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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