VMD-L Mailing List

From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Thu Apr 23 2009 - 12:22:38 CDT

In this study,

 W. Song, R. Biswas and M. Maroncelli. Intermolecular interactions
 and local density augmentation in supercritical solvation: A survey of
 simulation and experimental results. Journal of Physical Chemistry A,
 104:6924-6939, 2000.

the concept of local density augmentation is explored in
the study of solutes in supercritical carbon dioxide.
 This other study provides some pictures of that effect, which
are illustrative:

http://dx.doi.org/10.1016/j.supflu.2004.11.020

You may want to use similar ideas.

Leandro.

On Thu, Apr 23, 2009 at 12:15 PM, Krishnan, Marimuthu
<krishnanm_at_ornl.gov> wrote:
> Dear friends,
>
> I would like to calculate the local packing density around a methyl group (or a side chain) of a protein.
> The MD trajectory, which was generated using NAMD, of this protein is available. I would appreciate if
> someone could direct me to some existing codes/scripts that can do this task.
>
> I would be happy to write a simple code to do this job but I need some clarifications on this topic.
> To compute local packing density, I need to know the vdW radii of the chemical group and its neighbors.
> I am wondering about contributions from bonded atoms (There is no van der Waals interactions between
> atoms involved in a covalent bond, angle and dihedral). The questions are:
> (1) How do I get vdW radii of the chemical group( or atoms) and its neighbors?
> (2) How do I take care of bonded pair of atoms in the computation of local packing density?
>
> I would appreciate your help and suggestions.
>
> Thanks,
> Krishnan
>
> *************************************************
>
> Dr. Marimuthu Krishnan
> Postdoctoral Research Scholar,
> Center for Molecular Biophysics,
> Oak Ridge National Laboratory,
> Building 6011,
> PO Box 2008 MS6309,
> Oak Ridge, TN 37831-6309,
> Tel :  001-865-574-6123
> Fax :  001-865-576-7651
> E-mail :  krishnanm_at_ornl.gov
> For more details : http://cmb.ornl.gov/group/kgh
> *************************************************
>
>
>