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<div class="moz-cite-prefix">But you didn't write which interactions
you want to exclude exactly. You write about groups, but that is
incorrect, interactions contribute to the virial, not atoms.<br>
I assume you want to exclude the solid-solid interactions. That
can be done by setting all solid-solid interaction parameters to
zero, assuming there are no charges. If there are charges, you can
use the old group cutoff-scheme with energy group exclusions.<br>
You write about solid-liquid interactions, but excluding those
would not result in a meaningful virial, I would think.<br>
<br>
Berk<br>
<br>
On 06/25/2015 05:15 PM, Hardy, Adam wrote:<br>
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<blockquote cite="mid:D1B1D91D.6B89%25ah259@hw.ac.uk" type="cite">
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<div>If we were able to make the changes we want then the
viral would be correct for what we need it for</div>
<div><br>
</div>
<div>We applied the freezing over restraints because the
restraints make other calculations substantially more
difficult but we might have to revisit that train of
thought.</div>
<div><br>
</div>
<div>Adam</div>
<div>
<div>----------------------------------------------------------</div>
<div>Adam Hardy</div>
<div>PhD Student</div>
<div>School of Engineering and Physical Sciences</div>
<div>Heriot Watt University</div>
<div>Edinburgh, EH14 4AS</div>
<div>Phone: +441314513074</div>
<div><a class="moz-txt-link-abbreviated" href="mailto:ah259@hw.ac.uk">ah259@hw.ac.uk</a></div>
<div>----------------------------------------------------------</div>
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<span style="font-weight:bold">From: </span><<a
moz-do-not-send="true"
href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>>
on behalf of Berk Hess <<a moz-do-not-send="true"
href="mailto:hess@kth.se">hess@kth.se</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a
moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>"
<<a moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 25 June
2015 16:12<br>
<span style="font-weight:bold">To: </span>"<a
moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>"
<<a moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re:
[gmx-developers] Modifying the shifted part of the viral<br>
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<div class="moz-cite-prefix">Hi,<br>
<br>
This can not be achieved easily.<br>
But in most cases the virial becomes meaningless when you
freeze particles.<br>
You might get meaningful results when you use (tight)
position restraints instead. Then you even have the option
to scale the COM of a tube along with pressure scaling, if
you want.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 06/25/2015 04:53 PM, Hardy, Adam wrote:<br>
</div>
<blockquote cite="mid:D1B1D466.6B82%25ah259@hw.ac.uk"
type="cite">
<div>
<div>Dear All,</div>
<div><br>
</div>
<div>I am simulating carbon nanotubes in solvent,
approximating the tubes as rigid cylinders using the
freeze group function to hold the CNT atoms in place.</div>
<div><br>
</div>
<div>To do this correctly I need to modify the virial. I
have already excluded the solid (frozen) groups from
the virial calculation but now what I require is to
exclude the shifted part of the virial calculation
(second part of equation B.11 in the gromacs manual)
for only the solid/fluid interactions. </div>
<div><br>
</div>
<div>My initial assessment is that it may be easier to
calculate this contribution after the fact and
subtract this from the total virial. The difficulty I
find is that in the part of the code where the virial
is calculated the forces have already been summed up
on each atom and I don’t see any way to access the
pairwise forces which I believe are necessary to do
what I want. I’ve looked at non-bonded force
calculations in the source code and it frankly scares
the hell out of me so I wouldn’t even know where to
start.</div>
<div><br>
</div>
<div>I am assuming there are no functions within the
code already that might allow me to do this.</div>
<div><br>
</div>
<div>Can anyone give me any suggestions? I guess ideally
I would be looking to find some sort of data structure
which contains all the pair-wise forces at some point
and I can work from there. Does this exist?</div>
<div><br>
</div>
<div><br>
</div>
<div>Many thanks,</div>
<div><br>
</div>
<div><br>
</div>
<div>Adam</div>
<div><br>
</div>
</div>
<div>
<div>----------------------------------------------------------</div>
<div>Adam Hardy</div>
<div>PhD Student</div>
<div>School of Engineering and Physical Sciences</div>
<div>Heriot Watt University</div>
<div>Edinburgh, EH14 4AS</div>
<div>Phone: +441314513074</div>
<div><a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:ah259@hw.ac.uk">ah259@hw.ac.uk</a></div>
<div>----------------------------------------------------------</div>
</div>
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