[gmx-developers] virial

[Jason de Joannis]

You are right. I will have to track down a good article which derives
the two virials, as I have only seen bits and pieces of the explanation 
here and there. From the 'force on the molecule' perspective, the 
angle, dihedral and even bond forces do not count.

/Jason

Quoting "Moore, Jonathan (J)" <JMoore2 at dow.com>:

>
> Obviously, I'm not the person to be answering these questions...but I 
> guess I wasn't surprised that the GROMACS "virial calculations" for 
> the atomic virial contain intramolecular contributions since the 
> forces on an atom (part of the atomic virial) include contributions 
> from both inter- and intra-molecular interactions.
>
> Thanks,
> Jonathan
>
> ____________________________
> Jonathan Moore, Ph.D.
> Research and Engineering Sciences - New Products
> Core R&D
> The Dow Chemical Company
> 1702 Building, Office 300E
> Midland, MI 48674  USA
> Phone:  (989) 636-9765
> Fax: (989) 636-4019
> E Mail: jmoore2 at dow.com
>
>
> -----Original Message-----
> From: gmx-developers-bounces at gromacs.org 
> [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of Jason de 
> Joannis
> Sent: Tuesday, November 21, 2006 3:41 PM
> To: gmx-developers at gromacs.org
> Subject: RE: [gmx-developers] virial
>
>
> 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.
>
> Also, the manual describes the SHAKE virial but what about LINCS?
>
> 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?
>
> /Jason
>
> Quoting "Moore, Jonathan (J)" <JMoore2 at dow.com>:
>
>> Jason,
>>
>> Perhaps GROMACS uses the atomic form of the virial rather than the
>> molecular form?
>>
>> Jonathan
>>
>> ____________________________
>> Jonathan Moore, Ph.D.
>> Research and Engineering Sciences - New Products
>> Core R&D
>> The Dow Chemical Company
>> 1702 Building, Office 300E
>> Midland, MI 48674  USA
>> Phone:  (989) 636-9765
>> Fax: (989) 636-4019
>> E Mail: jmoore2 at dow.com
>>
>>
>> -----Original Message-----
>> From: gmx-developers-bounces at gromacs.org
>> [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of Jason de
>> Joannis
>> Sent: Monday, November 20, 2006 5:50 PM
>> To: gmx-developers at gromacs.org
>> Subject: [gmx-developers] virial
>>
>>
>> I am trying to understand the virial calculations in order to zero
>> the contributions from certain atoms. As I see it, only pairwise
>> forces should be included and not things like dihedral forces. Is
>> that correct? The code looks like it uses the entire force on every
>> particle.
>>
>> --
>> \ Jason de Joannis  \
>> \ Emory University  \
>>  \ jdejoan at emory.edu \
>>   \ 404-402-1332      \
>>
>>
>
>
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-- 
\ Jason de Joannis  \
\ Emory University  \
  \ jdejoan at emory.edu \
   \ 404-402-1332      \