Re: [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”?

From: Christina Bergonzo <>
Date: Wed, 3 Mar 2021 09:17:30 -0500


I've attached the potential energy surface to this email.

The potential energies were generated with the GB-HCT model (igb=1, with
mbondi radii set), ff99SB force field.

Restrained energy minimization was performed at 2 degree intervals over the
entire phi/psi plane, using 50 kcal mol-1 rad-2 restraint forces on the phi
and psi angles. 500 steps of steepest descent minimization were followed by
500 steps conjugate gradient minimization. (

The potential energy surface is in a matrix format. If you use gnuplot, you
can view it using set pm3d map, and splot "File" matrix.


On Tue, Mar 2, 2021 at 11:10 PM Li Dailin <> wrote:

> Hi,
> I am trying the NEB tutorial (“Tutorial 6.6 Nudged Elastic Band (NEB)
> simulations”) on the Amber homepage. In the end of Section 7, the Phi-Psi
> value along with the potential energy surface was drawn. I am wondering how
> the figure was done since only 32 Phi-Psi-Energy dots were obtained from
> Section 1 to 6. Where the other energy data come from and how to extract
> them from files? Thanks a lot for your reply.
> Best,
> Dailin
> _______________________________________________
> AMBER mailing list

Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST

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Received on Wed Mar 03 2021 - 06:30:03 PST
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