Tutorial of GaMD in NAMD

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
accelMDGirest   0
accelMDGntcmd   1000000
accelMDGnteb    25000000
accelMDGntcmdprep       200000
accelMDGntebprep        200000
accelMDOutFreq  $dcdfreq
accelMDGsigma0P 6.0
accelMDGsigma0D 6.0
accelMDGrestfile        ${molname}-out.restart.gamd

run 26000000

Job #2: GaMD production simulation

accelMD         on
accelMDdual     on
accelMDdihe     on
accelMDG        on
accelMDGiE      1
accelMDGRestart on
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

accelMD         on
accelMDdual     on
accelMDdihe     on
accelMDG        on
accelMDGiE      1
accelMDGRestart on
accelMDGcMDSteps        0
accelMDGEquiSteps       0
accelMDGcMDPrepSteps    0
accelMDGEquiPrepSteps   0
accelMDOutFreq  $dcdfreq
accelMDGsigma0P 6.0
accelMDGsigma0D 6.0
accelMDGRestartFile     ${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.


Copyright Reserved © Yinglong Miao
Last updated: Sun, October 1, 2017