you can do it as following<div><br></div><div>1. create index file make_indx -f conf.gro -n index.ndx ( select VS and any other atoms you want lets say OTHERS)</div><div>2. in .mdp define energygrps "VS OTHERS"</div>
<div>3. exclude interactions by specifying energygrp_excl VS OTHERS in .mdp file</div><div><br></div><div>for more you can refer to manual..</div><div><br></div><div>I hope it helps</div><div><br></div><div>--</div><div>sikandar</div>
<div><br></div><div><br><div><div><div><br><div class="gmail_quote">On Thu, May 5, 2011 at 11:00 AM, Gavin Melaugh <span dir="ltr"><<a href="mailto:gmelaugh01@qub.ac.uk">gmelaugh01@qub.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Sikandar<br>
<br>
Cheers. How do you actually define the energy groups?<br>
<br>
Gavin<br>
<div class="im"><br>
Sikandar Mashayak wrote:<br>
> yes, you can make virtual sites interact with only specific sites by<br>
> using Energy Exclusion between energy groups. This can be done by<br>
> defining energy groups for virtual sites and other atoms, then exclude<br>
> or include the non-bonded interactions between them accordingly...<br>
><br>
> On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh <<a href="mailto:gmelaugh01@qub.ac.uk">gmelaugh01@qub.ac.uk</a><br>
</div><div class="im">> <mailto:<a href="mailto:gmelaugh01@qub.ac.uk">gmelaugh01@qub.ac.uk</a>>> wrote:<br>
><br>
> Hi All<br>
><br>
> Is it possible to have a virtual site interact with only specific<br>
> atoms<br>
> and not interact at all with everything else?<br>
><br>
><br>
> Cheers<br>
><br>
> Gavin<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
</div>> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<div class="im">> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
</div>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>
<div class="im">> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
><br>
<br>
</div>--<br>
<div><div></div><div class="h5">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br></div></div></div></div>