[gmx-users] problem with pull direction

[Thomas Schlesier]

>
> 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
> Message-ID:
>         <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.
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: huifangliu1985 at 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
>
> ------------------------------
>
>