[gmx-developers] Modifying the shifted part of the viral

Hardy, Adam ah259 at hw.ac.uk
Thu Jun 25 16:53:47 CEST 2015

Dear All,

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.

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.

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.

I am assuming there are no functions within the code already that might allow me to do this.

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?

Many thanks,


Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot Watt University
Edinburgh, EH14 4AS
Phone: +441314513074
ah259 at hw.ac.uk

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