[gmx-users] Pull.pdo Columns

Thomas Schlesier schlesi at uni-mainz.de
Mon Oct 6 13:10:56 CEST 2008

> Message: 1
> Date: Sun, 5 Oct 2008 09:51:23 -0400
> From: "VENKATESH HARIHARAN" <vuh105 at psu.edu>
> Subject: [gmx-users] Pull.pdo Columns
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1223214683l.995352l.0l at psu.edu>
> Content-Type: text/plain; charset="utf-8"
> Hello,
>      I understand this topic has been dealt with previously, and I have read
> all the relative material from the archives, but I am still having trouble
> deciphering what each column corresponds to in the pull.pdo file for an AFM
> pull, with one pull group and one reference group, and pulling in only the X
> direction.  From what I've read, the columns are as follows:
> Time RefX RefY RefZ PullX PullY PullZ SpringX SpringY SpringZ
the columns should be (in GORMACS 3.3.3)
Time   RefX   RefY   RefZ   PullX   SprX   PullY   SprY   PullZ   SprZ
you can check this, the pulldir+RefX should be SprX and so on...
> ...for a total of 10 columns.  The problem is that when I use the values of for
> the reference group and pull group at time zero to calculate end to end
> distance, they do not correspond to my starting pdb file after solvation.  Any
> thoughts?
> ______________________________
> Venkatesh Hariharan
> Pennsylvania State University
> Schreyer Honors College
> Undergraduate - Bioengineering
> "You must be the change you wish to see in the world."
> --Mohandas Karamchand Gandhi
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