[gmx-developers] virial

[Moore, Jonathan (J)]

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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