GaMD with nucleotides

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jan 23 2020 - 09:30:57 CST

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Hello
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
accelMDGRestartFile gamd-01.restart.game

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?

thanks
francesco pietra

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