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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>
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<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>
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<div>Adam</div>
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<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>ah259@hw.ac.uk</div>
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<span style="font-weight:bold">From: </span><<a 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 href="mailto:hess@kth.se">hess@kth.se</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>" <<a 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 href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>" <<a 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>
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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>
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Cheers,<br>
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Berk<br>
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On 06/25/2015 04:53 PM, Hardy, Adam wrote:<br>
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<blockquote cite="mid:D1B1D466.6B82%25ah259@hw.ac.uk" type="cite">
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<div>Dear All,</div>
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<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>
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<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>
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<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>
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<div>I am assuming there are no functions within the code already that might allow me to do this.</div>
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<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>
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<div>Many thanks,</div>
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<div>Adam</div>
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<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>
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