hey<div><br></div><div>another approach to do this without using energy group exclusion is to define non-bonded interactions parameter explicitly between atoms in ffnonbonded.itp file. You can specify sigma and epsilon to be zero in virtual sites atoms definition and specify individual pair interactions parameters using non-bonded interactions like following ...</div>
<div><br></div><div><div>; virtual site</div><div>VS1 0 0 0 D 0 0</div><div>VS2 0 0 0 D 0 0</div><div>VS3 0 0 0 D 0 0</div>
<div><br></div><div>[ nonbond_params ]</div><div>VS1 C 1 1.0 0.25</div><div>VS2 C 1 1.0 0.25</div><div>VS2 C 1 1.0 0.25</div><div><br></div><div>
--</div><div>sikandar</div><br><div class="gmail_quote">On Thu, May 5, 2011 at 11:47 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 Justin<br>
<br>
I do not intend to have charges on the sites. All I want is;<br>
when a CH3 group gets close to the site it feels a repulsive force. I<br>
have calculated a sigma and epsilon value for this interaction.<br>
<div class="im"><br>
Gavin<br>
<br>
Justin A. Lemkul wrote:<br>
><br>
><br>
</div><div class="im">> Gavin Melaugh wrote:<br>
>> Hi Justin<br>
>><br>
>> I am reading the manual at the moment. I want to include some virtual<br>
>> sites in my molecule so that only surrounding CH3s atom type C3 interact<br>
>> with then. All other atoms I don't want to interact with them. Do I<br>
>> create energy groups in the index file called say "virtual sites" and<br>
>> "exclusions", and list all the indices of the atom types that I don't<br>
>> want to interact with the virtual site in one group and all the virtual<br>
>> sites in another.<br>
>> e.g<br>
>><br>
>> [virtual sites]<br>
>> 17 18 19 20<br>
>><br>
>> [virtsite_exclus]<br>
>> 1 2 3 4 5 6 7 8 9 .....<br>
>><br>
><br>
> In a general sense, yes, that's the right approach. Note that if any<br>
> of these sites is charged and/or you're using PME, then this whole<br>
> exclusion thing goes out the window, as has been discussed several<br>
> times in recent days. Using energygrp_excl applies only to<br>
> short-range nonbonded interactions. If you need complete exclusion,<br>
> you may have to look into tabulated potentials if this is the case.<br>
><br>
> -Justin<br>
><br>
<br>
--<br>
</div><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>