[gmx-users] Questions about Pull Code

Jennifer Casey jrcasey20 at gmail.com
Thu Jan 28 02:06:01 CET 2010


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.

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