[gmx-users] Re: distance/direction PMF

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi all
> 
> Could someone please get back to me on this. I have ran two sets of
> umbrella sampling simulations
> 1- Using pull_geometry = distance, and pull_dim = Y Y Y
> 2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125
> 0.735968
>  
> In both cases I wish to calculate the PMF for taking a host out of a
> guest. I specify the distance between the COM of the two groups in the
> respective mdp files. The two curves I get are completely different
> which has leads me to ask a couple of questions:
> 

You're doing two different things here, so I'd suspect that you're going to get 
a different answer with different settings.

> 1) Does the vector change as the dynamics evolves (i.e is it just
> relative between the two points) or does it remain fixed in space?
> 

It is relative.

> 2) Using umbrella sampling in the second case does the relative position
> of the pull group (guest) fluctuate about the distance along the
> specified vector?
> 

Yes.

> Note- I couldn't run g_wham with pull_geometry = direction in my current
> version of gromacs, so I ran it in 4.5.3 but I had to use the -if
> pullf-files.xvg option.
> 

We'll have to assume that your "current version" is something in the 4.0.x 
series, so this outcome is expected.

http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force

> Some help would be appreciated as I have to be sure of what the program
> is actually doing.
> 

There's always the code :)

-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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