Hi,
are you sure that you want to have pull_dim = Y Y Y (which is the
default)? When you want to pull only in z direction, I would use
pull_dim = N N Y. Otherwise, your z coordinate is not your reaction
coordinate.
If you want to pull in 3 dimensions you probably want to use
pull_geomery=distance.
Hope this helps,
Jochen
Am 11/4/12 7:17 PM, schrieb David Peeler:
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:
# UMBRELLA 3.0
# 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
potential.
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.
Thanks,
David Peeler
Matysiak Biomolecular Modeling Laboratory
Fischell Department of Bioengineering
University of Maryland, College Park
--
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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