[gmx-users] steered MD simulation for calculating the PMF

[Justin A. Lemkul]

lammps lammps wrote:
> Hello,
> 
> I want to use the Steered molecular dynamics simulations to calculate 
> the PMF with Gromacs.
> 
> How could I write the pull code? Are there some examples?
> 

There are some in the list archives that people have posted.

> And what files the GMX will create when running the SMD code? Then how 
> to obtain the PMF after full running? Is there any command for this?
> 

The pull code generates pullf.xvg and pullx.xvg within each umbrella sampling 
window.  These files, along with the .tpr files used to create them, are the 
input into g_wham, which runs the WHAM method for calculating PMF.

-Justin

> Thanks in advance.
> 
> -- 
> wende
> 

-- 
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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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