[gmx-users] Umbrella Sampling and Electric Field
agnivogromacs14 at gmail.com
Tue Nov 25 19:23:08 CET 2014
I have calculated the free energy of binding between a DNA and a protein by
using the umbrella sampling method as laid out in Dr. Lemkul's tutorial.
Now , I wish to apply electric field along the direction of pulling and see
its effects on the biomolecules as well as the PMF.
I am thinking about applying the field only during the SMD i.e. steered
molecular dynamics run and during the umbrella sampling simulations on each
of the extracted windows.
I am not applying the field during any of the restrained equilibration
steps i.e. before the SMD or the short NPTs before the umbrella sampling
But , I am unable to find support for my theory in the GROMACS 4.6.7
manual. It only tells how to set the electric field but does not talk about
its application and possible artifacts arising out of it.
Does anybody have any advice or suggestions. Please share.
Thanks & Regards
Grad Student, Iowa State University.
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