[gmx-users] g_wham with pull_geometry=position

[David Peeler]

Hi, thanks for your response,

Since I'm using pull_geometry=position I was under the impression that
defining pull_dim was not necessary.
Instead, I defined pull_vec to specify that the protein should be pulled
along <0 0 1>
I was previously using pull_geometry=distance with pull_dim= N N Y but
found that at slow pull_rates the protein actually moved in the opposite
direction that I wanted. I am using a negative pull_k but from what I've
read that is fine.
I will try to use pull_dim along with the pull_vec definition while
using pull_geometry=position, I just thought the two were mutually
exclusive.

Thanks,
David

On Tue, Nov 6, 2012 at 8:08 AM, Jochen Hub <jhub at gwdg.de> wrote:

> 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/ <http://cmb.bio.uni-goettingen.de/>
> ------------------------------**---------------------
>



-- 
David Peeler <http://www.linkedin.com/pub/david-peeler/3b/b4b/123>
President,* *Society of Biological Engineers
University of Maryland, College Park '13