Re: GaMD with nucleotides

From: Miao, Yinglong (
Date: Thu Jan 23 2020 - 13:42:09 CST

Hello Francesco,

The number of equilibration steps indeed look too small to me. More importantly, you want to check the effective harmonic force constants k0P and k0D in the output file to see whether they level off. You may also analyze the boost potential in terms of the average and standard deviation to check whether you have obtained reasonable/optimal acceleration.

You can find more details on these webpages:

All the best,

Yinglong Miao, Ph.D.
Assistant Professor
Center for Computational Biology and
Department of Molecular Biosciences
University of Kansas
Tel: 1-785-864-8298

On Jan 23, 2020, at 9:30 AM, Francesco Pietra <<>> wrote:

I am seeking advice on GaMD parameters for nucleotides. An assembly of nucleotides proved stable under NPT CHARMM36, while subsequent GaMD led to poor rmsd. The parameters I used or these preliminary assays with GaMD were:

accelMD on
accelMDdihe on
accelMDdual on
accelMDOutFreq 10
accelMDG on
accelMDGcMDPrepSteps 25000
accelMDGcMDSteps 50000
accelMDGEquiPrepSteps 25000
accelMDGEquiSteps 10000
accelMDGRestart off

The number of steps is very much shortened, albeit in scale with successful GaMD with proteins. Is such drastic shortening the reason for poor performance?

francesco pietra

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:08 CST