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

[Berk Hess]

But you didn't write which interactions you want to exclude exactly. You 
write about groups, but that is incorrect, interactions contribute to 
the virial, not atoms.
I assume you want to exclude the solid-solid interactions. That can be 
done by setting all solid-solid interaction parameters to zero, assuming 
there are no charges. If there are charges, you can use the old group 
cutoff-scheme with energy group exclusions.
You write about solid-liquid interactions, but excluding those would not 
result in a meaningful virial, I would think.

Berk

On 06/25/2015 05:15 PM, Hardy, Adam wrote:
> 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
>> ----------------------------------------------------------
>>
>>
>>
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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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