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Hello,<br>Unfortunately I still don't understand the equations in the manual after reading Chapter 2 of <span><span class="authors">Hendrik Bekker's dissertation. In that chapter, the virial is expressed as A+B+C.</span>
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 </span>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.<br>Anyone has an idea about it?<br>Thanks,<br>Lanyuan<br><br>> Date: Wed, 12 Aug 2009 22:01:14 +0200<br>> Subject: Re: [gmx-users] A question regarding single sum virial<br>> From: tsjerkw@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Hi Lanyuan Lu,<br>> <br>> It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available at:<br>> http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/<br>> <br>> Cheers,<br>> <br>> Tsjerk<br>> <br>> 2009/8/12 LuLanyuan <lulanyuan@msn.com>:<br>> > Hello all,<br>> > I got a question when I read the the manual chapter for the single sum<br>> > virial (p195-196). In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't<br>> > delta here also depend on index j? I think delta is zero when particle i and<br>> > j are close. And delta can be something else when any x/y/z component of<br>> > r_i-r_j is larger than half box length. But from eq (B.5) to (B.11) it seems<br>> > delta_i only depends on index i and I got confused.<br>> > Could anyone explain it to me?<br>> > Thanks very much!<br>> > Lanyuan Lu<br>> ><br>> > ________________________________<br>> > 使用新一代 Windows Live Messenger 轻松交流和共享! 立刻下载!<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> <br>> <br>> <br>> -- <br>> Tsjerk A. Wassenaar, Ph.D.<br>> Junior UD (post-doc)<br>> Biomolecular NMR, Bijvoet Center<br>> Utrecht University<br>> Padualaan 8<br>> 3584 CH Utrecht<br>> The Netherlands<br>> P: +31-30-2539931<br>> F: +31-30-2537623<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />您可以借助 Windows Live 整理、编辑和 <a href='http://www.microsoft.com/china/windows/windowslive/products/photo-gallery-edit.aspx' target='_new'>共享您的照片。</a></body>
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