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

Berk Hess hess at kth.se
Thu Jun 25 17:11:49 CEST 2015


This can not be achieved easily.
But in most cases the virial becomes meaningless when you freeze particles.
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.



On 06/25/2015 04:53 PM, Hardy, Adam wrote:
> 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
> ----------------------------------------------------------
> 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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