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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>
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<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 class="moz-txt-link-abbreviated" href="mailto:ah259@hw.ac.uk">ah259@hw.ac.uk</a></div>
<div>----------------------------------------------------------</div>
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