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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>ah259@hw.ac.uk</div>
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