On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman <[email protected]>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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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