> > Message: 1 > Date: Sat, 14 Mar 2009 10:41:46 +0800 > From: huifang liu <huifangliu1...@gmail.com> > Subject: [gmx-users] problem with pull direction > To: gmx-users@gromacs.org > Message-ID: > <e523c6be0903131941oa428a3eo138323abc8067...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello gmx-users, > > I find the pulling direction in PULL INFO section of the log file is not > coincident with the afm_dir1 parameter i defined in the pull.ppa. could some > one tell me which direction is actually used in the pulling process? > >From the pull.ppa it looks you are using version 3.x ? there you must give GROMACS the pull direction as an normalized vector. I believe to remember that in the log-file the direction becomes normalized, but the great problem is, the pull velocity uses afm_dir1(so if afm_dir1 is not normalized your pull velocity becomes wrong). I would say look at both vectors (in .ppa and log-file) and look what they become if you normalise them. Hope that this helped. Thomas > Thank you very much. > > > Huifang Liu > > -- > Huifang Liu (Ph.D. Student) > School of Pharmacy > Fudan University > > 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) > Shanghai, China, 200032 Cell phone: +86-13764669357 > E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090314/023ffc8d/attachment-0001.html > > ------------------------------ > >
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