[gmx-users] Questions about Pull Code

[Justin A. Lemkul]

Jennifer Casey wrote:
> Hello,
> 
> I am a new Gromacs user, and I could really use some clarification about 
> the pull code.  I am interested in creating the PMF for Na+ and I- in 
> the presence of THF.  I saw a previous posting that the best way to go 
> about creating the PMF is:
> 1)  Generate a trajectory of configurations along the reaction coordinate.
> 2)  Use the difference configurations as starting points for independent 
> simulations in sampling window.
> 3)  Use umbrella sampling to constrain in window.
> 4)  Use g_wham to construct PMF
> 
> This is how I am interpreting the instructions, but could you please let 
> me know if I am correct in my assumptions?  First I create a couple of 
> unique starting configurations, with Na+ and I- separated by specific 
> distances.  Once that has been done, I take one such configuration and 
> turn on the options under com_pulling (especially pull_geometry = 
> umbrella) in the .mdp file.  I let this run for some amount of time, and 
> end up with a pullx.xvg and a pullf.xvg file.  I do this with the other 
> configurations as well.  Once that has been done, I take all of these 
> .xvg and .tpr files and create a .dat file, which can be used with 
> g_wham to construct the PMF.
> 
> I really appreciate the help.  Nobody in my lab has done this before, 
> and I am feeling pretty unsure of myself.
> 

In general, yes, you've got the right procedure.  Coincidently, I have just 
created a PMF/umbrella sampling tutorial that is linked from the "Tutorials" 
page on the Gromacs site.  The system in the tutorial is certainly more 
complicated than what you're looking to do, but still might be of use.

-Justin

> Thanks.
> 

-- 
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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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