[AMBER] Problem with CG minimization in implicit solvent

From: Alejandro Gil Ley <alejandro.gilley.zymeworks.com>
Date: Wed, 10 Mar 2021 19:17:05 +0000

Dear Amber Community

I found a peculiar pattern in the forces and energy as a function of the minimization steps while running minimizations with pmemd and sander using conjugate gradient in implicit solvent, in Amber20.
After the first initial steps using steepest descent, CG energies and forces exhibited frequent jumps of several orders of magnitude as the minimization progressed.
To demonstrate this issue here I used alanine-dipeptide. All the input files needed to reproduce this data are attached.
I tried different systems, like DNA and TRP cage, and changed the frequency of nonbonded list updates nsnb, but the problem remained.

Below I have plotted, as a function of the minimization step, the maximum force and the difference between the system energy and the minimum energy (plus a constant).
For this example I used ntmin = 1, ncyc = 100, nsnb = 25 and cut = 9999. You can see that energies decrease monotonically for the first 100 steepest descent steps,
but then immediately after, frequent jumps in forces and energy of several orders of magnitude appear. Example is shown for pmemd and sander.
If the xmin minimizer is used with PRCG then the issue disappears.

I could do a full minimization using steepest descent and ignore this problem,
but I would like to know whether someone has encountered this problem before.
Is this a known issue with conjugate gradient in implicit solvent?

Thanks in advanced for your help,

Alejandro Gil



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Received on Wed Mar 10 2021 - 11:30:02 PST