<div dir="ltr">Right. Well, charge groups should be illegal :-P<div><br></div><div>Mark</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 12, 2014 at 7:34 PM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>No, with charge groups you do need a
buffer, grompp will even warn you about this.<span class="HOEnZb"><font color="#888888"><br>
<br>
Berk</font></span><div><div class="h5"><br>
<br>
On 09/12/2014 07:32 PM, Mark Abraham wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">True for the first part, but rerun does not ever
need a buffer, because neighbour search is every frame.
<div><br>
</div>
<div>Mark</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Sep 12, 2014 at 7:30 PM, Berk
Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
You can use the group scheme for the rerun only. If you use
the same potential modifiers and add a buffer to rlist, you
should get exactly the same answer as the Verlet scheme.<br>
<br>
We should come up with a way to do this with the Verlet
scheme when we remove the group scheme.<br>
<br>
Cheers,<br>
<br>
Berk
<div>
<div><br>
<br>
On 09/12/2014 05:20 PM, Bernd Doser wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Berk,<br>
<br>
thanks for your answer. We store force contributions
between two atoms<br>
to analyze them. This storage will be performed during
a rerun. We want<br>
to exclude the unneeded interactions to speed-up the
rerun, since we are<br>
only interested in forces between two atom groups.<br>
<br>
Cheers,<br>
Bernd<br>
<br>
On 09/12/2014 04:21 PM, Berk Hess wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
Why do you need to exclude energy group interactions
during rerun?<br>
Since you will have all the energy group pair
contributions you can<br>
manually subtract the terms you want to exclude. You
wouldn't even need<br>
a rerun for that if you used the energy groups for
the production run.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 09/12/2014 03:26 PM, Bernd Doser wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear GROMACS developers,<br>
<br>
As the energy group exclusions are not implemented
for the Verlet cutoff<br>
scheme, I am search for a alternative possibility
to exclude specific<br>
nonbonded interactions during an md rerun.<br>
<br>
One idea is to use the topology exclusion list.
The top->excl arrays<br>
could be modified for example at the beginning of
do_force() in<br>
sim_util.c. I have tested it for a small protein
and a water dimer and<br>
it works. Is there any problem doing this for more
complex structures or<br>
have anyone a better idea to exclude nonbonded
interactions to reduce<br>
computation time?<br>
<br>
Thank you very much in advance!<br>
<br>
Best regards,<br>
Bernd Doser<br>
<br>
</blockquote>
</blockquote>
</blockquote>
<br>
-- <br>
</div>
</div>
<div>
<div>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a>
before posting!<br>
<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>
<br>
* For (un)subscribe requests visit<br>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a>
or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
<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>
<br>
* For (un)subscribe requests visit<br>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br></div>