<br><br><div class="gmail_quote">On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman <span dir="ltr"><<a href="mailto:jadelman@berkeley.edu">jadelman@berkeley.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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.</blockquote>
<div><br></div><div>We use the ASN server from Ivet Bahar's group and get nice results. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
<br>
Right now I am looking for suggestions on how to explicitly turn off all non-bonded interactions (the only FF terms are bonded terms).</blockquote><div><br></div><div>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)</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"> Is the best option to use energygrp excl? Any other useful suggestions for using gromacs for this purpose would also be appreciated.<br>
<br>
Josh<br>
<br>
<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use thewww interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br>