[gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi Justin
> 
> Many thanks for the reply I know technically I am doing two different
> things. However due to my starting conifgurations in both cases I would
> expect similar results.
> Could you confirm the following points
> 
> 1) In pull_geometry=distance, and pull_dim =YYY; is the absolute
> distance between the COM of both groups in all directions considered ?
> 

Yes.

> 2) In pull_geometry = direction, with a specified vector; I assume that
> it is the distance between the two groups along this vector that is
> considered?
> 

Should be.  Compare the output of g_dist with what grompp reports as the initial 
distance.

> 3) Is the specified vector taken to be the vector connecting the two
> points? Therefore are the desired distances in the mdp files essentially
> the magnitudes of this vector at each window.
> 

Per the documentation, grompp normalizes the vector, so no, not directly.  But 
if you have proper settings for pull_init/pull_start, then the reference 
distance should be correctly calculated along the specified vector for each window.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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