[gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Justin
> 
> I did a short test on a particular window with the specified vector with
> pull_init =0.78nm. I then grompp(ed) the final configuration and it gave
> me a distance of 0.78 as the initial ditsance, fair enough. However when
> I viewed the final line from g_dist the absolute distance or modulus was
> 0.815 nm, which agreed with the distance I calculated using a molecular
> configuration editor. My question is therefore this, when using
> pull_geometry =direction with a specified vector, How should one
> interpret the initial distance provided by grompp? and how does Gromacs
> deal with the fact that the vector between the two point changes during
> the run ?
> 

You're telling grompp that the initial distance is 0.78 nm, so it's spitting 
that back out.  If that's not the true distance, then specify the correct 
quantity :)  The distance should be correctly detected with:

pull_start = yes
pull_init = 0

As for the second question, the vector doesn't change over the simulation, but 
the position of pull_group1 along that vector will.  That's what the umbrella 
potential is doing - it allows for harmonic oscillation along any of the 
dimensions specified by pull_vec/pull_dim (depending on the settings).

-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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