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

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 22 12:52:48 CET 2009

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.


> Thanks in advance.
> -- 
> wende


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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