[gmx-users] Pull.pdo Columns

VENKATESH HARIHARAN vuh105 at psu.edu
Sun Oct 5 15:51:23 CEST 2008


     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

...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


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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