From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Jun 07 2010 - 06:17:34 CDT
You have right Neelanjana, providing that definition of one side-chain
in each desired region of the protein will speed up computation
significantly, and you should obtain very comparable results, as for
definition of many side chains in each region.
Branko
On 6/7/2010 10:07 AM, Neelanjana Sengupta wrote:
> Dear NAMD community,
>
> When the collective variable is a 'distance' between 2 atom groups,
> each containing more than one atom (eg. the sidechains of two regions
> of a protein), am I right in assuming that the distance refers to the
> centers of mass distance of the two groups?
>
> Thanks,
> Sengupta
>
>
>
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