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 聽 聽 聽 聽 on
accelMDdual 聽 聽 on
accelMDdihe 聽 聽 on
accelMDG 聽 聽 聽 聽on
accelMDGiE 聽 聽 聽1
accelMDGRestart聽 off
accelMDGStatWindow聽 20000
accelMDGcMDSteps聽 1000000
accelMDGEquiSteps聽 聽25000000
accelMDGcMDPrepSteps聽 聽 聽 200000
accelMDGEquiPrepSteps聽 聽 聽 聽200000
accelMDOutFreq 聽$dcdfreq
accelMDGsigma0P 6.0
accelMDGsigma0D 6.0
accelMDGRestartFile 聽 聽 聽 ${molname}-out.restart.gamd
run 26000000
Job #2: GaMD production simulation
accelMD 聽 聽 聽 聽 on
accelMDdual 聽 聽 on
accelMDdihe 聽 聽 on
accelMDG 聽 聽 聽 聽on
accelMDGiE 聽 聽 聽1
accelMDGRestart on
accelMDGStatWindow聽 20000
accelMDGcMDSteps 聽 聽 聽 聽0
accelMDGEquiSteps 聽 聽 聽 0
accelMDGcMDPrepSteps 聽 聽0
accelMDGEquiPrepSteps 聽 0
accelMDOutFreq 聽$dcdfreq
accelMDGsigma0P 6.0
accelMDGsigma0D 6.0
accelMDGRestartFile 聽 聽 ${molname}-out.restart.gamd
reinitvels $temperature
run 25000000
Job #3: repeat running jobs using this input file until end of your GaMD production simulation
accelMD 聽 聽 聽 聽 on
accelMDdual 聽 聽 on
accelMDdihe 聽 聽 on
accelMDG 聽 聽 聽 聽on
accelMDGiE 聽 聽 聽1
accelMDGRestart on
accelMDGStatWindow聽 20000
accelMDGcMDSteps 聽 聽 聽 聽0
accelMDGEquiSteps 聽 聽 聽 0
accelMDGcMDPrepSteps 聽 聽0
accelMDGEquiPrepSteps 聽 0
accelMDOutFreq 聽$dcdfreq
accelMDGsigma0P 6.0
accelMDGsigma0D 6.0
accelMDGRestartFile 聽 聽 ${molname}-out.restart.gamd
run 25000000
Note: You can also perform multiple independent GaMD simulations with randomized atomic velocities by repeating jobs #2 and #3.