[gmx-users] problem with pull direction
schlesi at uni-mainz.de
Mon Mar 16 11:49:44 CET 2009
> Message: 1
> Date: Sat, 14 Mar 2009 10:41:46 +0800
> From: huifang liu <huifangliu1985 at gmail.com>
> Subject: [gmx-users] problem with pull direction
> To: gmx-users at gromacs.org
> <e523c6be0903131941oa428a3eo138323abc80678f4 at 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.
> 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: huifangliu1985 at gmail.com Fax: (86-21)54237264
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