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<div class="moz-cite-prefix">No, with charge groups you do need a
buffer, grompp will even warn you about this.<br>
<br>
Berk<br>
<br>
On 09/12/2014 07:32 PM, Mark Abraham wrote:<br>
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<div dir="ltr">True for the first part, but rerun does not ever
need a buffer, because neighbour search is every frame.
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<div>Mark</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Sep 12, 2014 at 7:30 PM, Berk
Hess <span dir="ltr"><<a moz-do-not-send="true"
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 class="HOEnZb">
<div class="h5"><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>
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-- <br>
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