Re: Implementation of ELASTIC NETWORK model in NAMD

From: Victor (
Date: Fri Aug 23 2013 - 12:29:01 CDT

I did this at some point in the past (though not for NAMD). Using
Matlab, I created parameter, topology and a CG coordinate files from the
all atom structures, at which point any MD package could be used. This
is easy, as the ENM model only has bonds. This could also be done in
VMD with some scripting. Such an approach is quite flexible (though it
might appear laborious at first); e.g. it allows you have multiple
protein subunits, each described by an ENM interacting via nonbonded LJ
or electrostatic interactions, should you choose to add charges to your
CG beads. I believe I've also modified nonbond exclusion lists in the
psf to avoid unwanted interactions (though you could get away without
doing this by setting a very short neighbor list radius, since there
would only be bonded atoms within such a cutoff). All of the above file
formats are described elsewhere online.


On 08/23/2013 11:57 AM, Vibhor Agrawal wrote:
> Hello All:
> I wanted to implement the elastic network course grain technique in my
> protein.I have been looking around way to implement it.Apart from
> webserver I didn't find any package in NAMD that can perform the
> analysis.It would be great if someone can direct me to resource or
> have done it in past and can help.
> Thanks alot:
> Vibhor

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