GaMD with nucleotides

From: Francesco Pietra (
Date: Thu Jan 23 2020 - 09:30:57 CST

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

francesco pietra

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