[gmx-users] Pull.pdo Columns

[Thomas Schlesier]

> 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>
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>
> 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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