[gmx-users] A question regarding single sum virial

LuLanyuan lulanyuan at msn.com
Wed Aug 12 23:51:47 CEST 2009


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
> >
> > ________________________________
> > 使用新一代 Windows Live Messenger 轻松交流和共享! 立刻下载!
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
您可以借助 Windows Live 整理、编辑和共享您的照片。
http://www.microsoft.com/china/windows/windowslive/products/photo-gallery-edit.aspx
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090812/86175314/attachment.html>


More information about the gromacs.org_gmx-users mailing list