Hi, Christina
Thanks for your reply and help.
Regards,
Dailin
-----邮件原件-----
发件人: Christina Bergonzo [mailto:cbergonzo.gmail.com]
发送时间: 2021年3月3日 22:18
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”?
Hello,
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. (
https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.22405)
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.
-Christina
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
>
--
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Fri Mar 05 2021 - 19:00:02 PST
