[gmx-users] g_wham with pull_geometry=position

[Jochen Hub]

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
>

-- 
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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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