[gmx-users] g_wham with pull_geometry=position

David Peeler dj.peeler at gmail.com
Sun Nov 4 19:17:56 CET 2012

Hello all,

My simulation involves the pulling of a protein in the negative direction
of the z-axis into a stationary hydrophobic self-assembled monolayer
surface model (MTHL) using the position pull geometry. My umbrella
parameters in the md_umbrella.mdp file are as follows:

pull            = umbrella
pull_geometry   = position
pull_vec1       = 0 0 1
pull_start      = yes
pull_ngroups    = 1
pull_group0     = MTHL
pull_group1     = Protein
;pull_init1     = 0
pull_rate1      = 0.0
pull_k1         = 500

My output pullf files have three dimensions in them because of the pull_vec
definition, so I wrote a script to calculate the magnitude of the pull
force and to return the files with a time column and a force column.

I was told by g_wham to make my own pdo files, but am struggling to do so;
it looks like I have to insert a header with all the umbrella information
for each run in the beginning of each file. I believe the header for my
files should look like this:

# Component selection: 0 0 1
# nSkip 1
# Ref. Group ’MTHL’
# Nr. of pull groups 1
# Group 1 'Protein’ Umb. Pos. Z Umb. Cons. 500

I'm not sure what nSkip means and I'm not sure what I should put for
Component selection. Can someone give me a quick tutorial or a script that
helps create pdo files?

I tried passing the files I created with the force magnitudes to g_wham as
normal pullf files (since those don't have strange headers); however, using
the -if option requires the -it option and those tpr files contain
information about the pull_vec that generates this output:

Fatal error:
Found pull geometry 'position' and more than 1 pull dimension (3).
Hence, the pull potential does not correspond to a one-dimensional umbrella

Is there a simpler way to do g_wham with position pull geometry?
I believe my intuition to calculate the magnitude of the force is correct
but would be interested to see if anyone thinks only the z-component of the
umbrella force is of interest.

David Peeler
Matysiak Biomolecular Modeling Laboratory
Fischell Department of Bioengineering
University of Maryland, College Park

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