Hello,
Thanks for your reply in details on the computation protocol.
Many thanks.
Dailin
-----邮件原件-----
发件人: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
发送时间: 2021年3月3日 22:20
收件人: AMBER Mailing List <amber.ambermd.org>
主题: Re: [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”?
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:
from
https://onlinelibrary.wiley.com/doi/full/10.1002/qua.22405
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
http://membrane.urmc.rochester.edu/Software/WHAM/WHAM.html).
On Tue, Mar 2, 2021 at 11:10 PM Li Dailin <lidl25.hotmail.com> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 05 2021 - 19:00:02 PST
