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

From: Carlos Simmerling <>
Date: Wed, 3 Mar 2021 09:19:36 -0500

the underlying energy map is not from the NEB calculation.
if you look in our Bergonzo et al. paper cited at the beginning of the
tutorial you can see this methods information:


A common way to calculate free energy using molecular dynamics is to use
the umbrella sampling technique. The free energy surface of the alanine
dipeptide system was calculated using umbrella sampling by first building
and minimizing independent structures where the phi and psi were rotated
every 5° to cover the complete periods (−180 to 180°) of both backbone
dihedrals, totaling 1,296 simulations. During the minimization process, the
phi and psi dihedrals were restrained with a force constant of 500 kcal
mol−1 rad−2 and the minimization was run for 1,000 steps. Each minimized
phi/psi structure was used as the starting structure of an independent
umbrella simulation, yielding 1,296 windows. The force constant for the
production dynamics was 75 kcal mol−1 rad−2 on the phi and psi dihedrals,
and each window was simulated for 10 ps at 300 K. The phi and psi values
were saved at every time step. Data was postprocessed into free energy
profiles using the WHAM 21-23, using a program provided by Alan Grossfield,
(freely available at

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
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Received on Wed Mar 03 2021 - 06:30:05 PST
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