GaMD-NAMD: Tutorial

Template input files for running GaMD in NAMD

In case you are running GaMD simulation on a computer cluster that imposes wallclock limit for simulation jobs, you may divide your long simulation into multiple jobs, which could include for example job #1 for 2 ns conventional MD (cMD) and 50 ns GaMD equilibration, job #2 for starting GaMD production simulation with radomized atomic velocities, and job #3 for extending GaMD production simulation until the end:

Job #1: cMD and GaMD equilibration

accelMD on
accelMDdual on
accelMDdihe on
accelMDG on
accelMDGiE 1
accelMDGRestart off
accelMDGStatWindow 20000
accelMDGcMDSteps 1000000
accelMDGEquiSteps 25000000
accelMDGcMDPrepSteps 200000
accelMDGEquiPrepSteps 200000
accelMDOutFreq $dcdfreq
accelMDGsigma0P 6.0
accelMDGsigma0D 6.0
accelMDGRestartFile ${molname}-out.restart.gamd

run 26000000

Job #2: GaMD production simulation

accelMD on
accelMDdual on
accelMDdihe on
accelMDG on
accelMDGiE 1
accelMDGRestart on
accelMDGStatWindow 20000
accelMDGcMDSteps 0
accelMDGEquiSteps 0
accelMDGcMDPrepSteps 0
accelMDGEquiPrepSteps 0
accelMDOutFreq $dcdfreq
accelMDGsigma0P 6.0
accelMDGsigma0D 6.0
accelMDGRestartFile ${molname}-out.restart.gamd

reinitvels $temperature
run 25000000

Job #3: repeat running jobs using this input file until end of your GaMD production simulation

run 25000000

Note: You can also perform multiple independent GaMD simulations with randomized atomic velocities by repeating jobs #2 and #3.