[gmx-developers] virial

[Jason de Joannis]

Quoting Erik Lindahl <lindahl at cbr.su.se>:

> Hi Jason,
>
Hi.
>> On Nov 21, 2006, at 9:41 PM, Jason de Joannis wrote:
>>
>> From the manual and the code, it looks like Gromacs uses the atomic
>> virial. I think that is besides the point.
>>
>> Why does Gromacs use f[i] which (I think) contains all bonded and  
>> nonbonded forces? After all the derivative resp. volume scaling  
>> vanishes for some of the bonded forces.
>
> Forces are forces are forces, which give rise to pressure. There is  
> no fundamental physical difference between bonded and nonbonded  
> interactions.
Hmm. I generally think from the partition function rather than 
mechanically. Anyways, why do you have Appendix B.1.4 which treats
the virial for harmonic bonds explicitely?
>
> Gromos (and some other codes) use whole-molecule-virials to reduce  
> the effect of some numerical errors, but there are other drawbacks  
> with this - primarily performance.
>
>>
>> Also, the manual describes the SHAKE virial but what about LINCS?
>
> We use "Shake virial" as a generic name for virial contributions from 
>  constraints, so it's identical for SHAKE and LINCS.
Okay, thats true. I can see real numbers when I print out shake_vir. That
means I will have to go inside LINCS and somehow zero the unwanted
virial terms.
>
>>
>> Also, where can I find a little more info on the fr->fshift  contribution.
>> On the mailing list archive someone explained that this comes from  
>> forces on the 27 unit cells. Is that explained in the manual or  
>> somewhere?
>>
>
> It's mentioned in the manual where we derive the expression for  
> single-sum-virial. The performance advantage of the single sum is  
> also the reason why we prefer the atomic virial, btw!
Well I must need a stronger prescription on my contact lenses because
I have been looking closely at that section. It seems to me that
Eq. B.11 is all calculated within the normal virial routine.
>
> Cheers,
>
> Erik
Thanks.


-- 
\ Jason de Joannis  \
\ Emory University  \
  \ jdejoan at emory.edu \
   \ 404-402-1332      \