Re: [AMBER] Single Point Energy: sander x python sander

From: David A Case <>
Date: Thu, 13 Jan 2022 12:37:01 -0500

On Thu, Jan 13, 2022, Alan wrote:
>In details:
> Python x Sander
>error angle : 0.48950 % 4.29874 x 4.27770
>error bond : 2.04820 % 0.75717 x 0.77300

If your bond and angle energies don't agree, then debugging should be much

Check things like doing a single-step minimiation instead of MD. But it
probably comes down to getting into the code and seeing what the python
gb_input is doing (in complete detail); I don't know that off the top of my
head. It's possible that the python interface is doing somthing like
setting SHAKE by default, which you are not doing in your sander calculation.

You might try a very small system to see if that helps find the differences.


AMBER mailing list
Received on Thu Jan 13 2022 - 10:00:02 PST
Custom Search