From: Miao, Yinglong (miao_at_ku.edu)
Date: Thu Jan 23 2020 - 13:42:09 CST
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.
Center for Computational Biology and
Department of Molecular Biosciences
University of Kansas
On Jan 23, 2020, at 9:30 AM, Francesco Pietra <chiendarret_at_gmail.com<mailto:chiendarret_at_gmail.com>> 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:
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?
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