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

From: Daniel Roe <>
Date: Wed, 25 Mar 2015 13:18:47 -0600

On Wed, Mar 25, 2015 at 12:47 PM, Jason Swails <> wrote:
> create a corresponding prmtop file for that new trajectory

FYI this can be done with the 'outprefix' keyword of the 'closest' command.


, 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).
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 25 2015 - 12:30:03 PDT
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