[gmx-users] A question regarding single sum virial

[LuLanyuan]

Hello,
Unfortunately I still don't understand the equations in the manual after reading Chapter 2 of Hendrik Bekker's dissertation. In that chapter, the virial is expressed as A+B+C. 
Here A+B is the r_i*F_i stuff, which can be considered as the virial without considering PBC. And the third term should correspond to the detla derm in the Gromacs manual, which is a correction due to PBC. However, in the dissertation the correction term is always related to pairwise forces F_ij in different ways to calculate it. In the manual, the correction term is written as delta_i*F_i, which is related to individual force on each atom only. I still have no idea for that how the magic delta can convert a pairwise force expression into an individual force expression.
Anyone has an idea about it?
Thanks,
Lanyuan

> Date: Wed, 12 Aug 2009 22:01:14 +0200
> Subject: Re: [gmx-users] A question regarding single sum virial
> From: tsjerkw at gmail.com
> To: gmx-users at gromacs.org
> 
> Hi Lanyuan Lu,
> 
> It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available at:
> http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/
> 
> Cheers,
> 
> Tsjerk
> 
> 2009/8/12 LuLanyuan <lulanyuan at msn.com>:
> > Hello all,
> > I got a question when I read the the manual chapter for the single sum
> > virial (p195-196).  In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't
> > delta here also depend on index j? I think delta is zero when particle i and
> > j are close. And delta can be something else when any x/y/z component of
> > r_i-r_j is larger than half box length. But from eq (B.5) to (B.11) it seems
> > delta_i only depends on index i and I got confused.
> > Could anyone explain it to me?
> > Thanks very much!
> > Lanyuan Lu
> >
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> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
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