Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte

From: Jason Swails <>
Date: Wed, 25 Mar 2015 14:47:02 -0400

> On Mar 25, 2015, at 2:40 PM, Subrata Paul <> wrote:
> Dear Jason
> I want to calculate vdw energy and electrostatic energy for the first
> solvation shell.
> Do lie command calculate the energy for FSS in amber 12 tools ?

Not easily. You will probably need to use the “closest” command in cpptraj to create a system that only has the first solvation shell, create a corresponding prmtop file for that new trajectory, then use the “lie” or “energy” commands on the resulting trajectory.

Alternatively you can simply use a very small cutoff, but the energies will be very noisy on account of the cutoff being a truly horrible approach to long-range electrostatics.

Note that “first solvation shell” is not really rigorously defined to my knowledge (although everybody “knows” what it is). So you need to use some algorithmic definition for selecting the atoms in the first solvation shell and go with that. Also note that energy is an extensive property, so if different frames have different numbers of waters *in* that first solvation shell, their energies will not be directly comparable (which is why the “closest” command is probably a better approach than the hard cutoff).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 25 2015 - 12:00:06 PDT
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