VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Jun 04 2014 - 13:54:51 CDT

What do you think a reasonable value would be? What NAMDEnergy
calculates are interaction energies within the forcefield. The charges
involved for Glu are large (~1), have opposite sign, and be near one
another in space. Plug that into Coulomb's law (the constant is 332.0636
kcal$\cdot$Å/(mol$\cdot$e^2 )), and the numbers you get will be large,
so I don't think the ~100 or so numbers you have are unreasonable. So
congratulations! You've calculated the energy! You now also see why the
numbers are hard to interpret.

Were you trying to calculate the strength of that specific hydrogen
bond? If so, I think you'll want to use another approach, perhaps by
doing a histogram of the contact distances.
-Josh Vermaas

On 6/4/14, 1:45 PM, Ramin Ekhteiari wrote:
> Hi dears,
>
> I am trying to calculate energy between one polar amino acid residue
> (GLU) and a small ligand using NAMD energy plugin during a course of
> MD trajectories, but I face with results as below, (the electrostatic
> energy values are not reasonable for a H-bond).
>
> Frame Time Elec VdW Nonbond Total
> 0 0 -105.632 -3.0657 -108.698 -108.698
> 1 1 -103.383 -3.9904 -107.373 -107.373
>
> Would be grateful for any comments,
>
> Cheers,
> Ramin.
>
>