[gmx-users] Elastic Network Model

[Joe Joe]

On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman <jadelman at berkeley.edu>wrote:

> I am interested in potentially using gromacs to do some calculations on an
> C-alpha based elastic network model of the protein that I'm working on. I'm
> curious if other users have done similar types of calculations, and if so,
> what protocol you used. I realize that there are a lot of webservers out
> there that do this calculation, but I want to be able to use a heterogeneous
> network of spring constants, and have a bit more flexibility than many of
> them allow. Gromacs seemed like it might be a good option for tackling this
> problem since it can calculate the Hessian and generate the normal modes
> from an arbitrary force field. it also had a bunch of nice analyses tools
> available as well.


We use the ASN server from Ivet Bahar's group and get nice results.

>
>
> Right now I am looking for suggestions on how to explicitly turn off all
> non-bonded interactions (the only FF terms are bonded terms).


Define the atom types in your top file, instead of #include ff***.itp  and
set the LJ and Q's to zero or set nrexcl to > then the number of atoms (not
exactly sure what this will do but you can give it a try)


> Is the best option to use energygrp excl? Any other useful suggestions for
> using gromacs for this purpose would also be appreciated.
>
> Josh
>
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090331/087d8f5d/attachment.html>