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

[Hardy, Adam]

If we were able to make the changes we want then the viral would be correct for what we need it for

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.

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

From: <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se>> on behalf of Berk Hess <hess at kth.se<mailto:hess at kth.se>>
Reply-To: "gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>" <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>
Date: Thursday, 25 June 2015 16:12
To: "gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>" <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>
Subject: Re: [gmx-developers] Modifying the shifted part of the viral

Hi,

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.

Cheers,

Berk

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<mailto:ah259 at hw.ac.uk>
----------------------------------------------------------



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----- 
We invite research leaders and ambitious early career researchers to 
join us in leading and driving research in key inter-disciplinary themes. 
Please see www.hw.ac.uk/researchleaders for further information and how
to apply.

Heriot-Watt University is a Scottish charity
registered under charity number SC000278.

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