gamd restart file in namd 2.13

From: Aravinda Munasinghe (
Date: Tue Dec 03 2019 - 08:17:20 CST

Dear All,
I am trying to run gamd within namd 2.13. I have been using keywords in to define associated
parameters needed for NAMD gamd setup. So, when I run the conventional MD
and GaMD equilibration step, I have the following parameters within the
namd section.
accelMD on
accelMDdual on
accelMDdihe on
accelMDG on
accelMDGiE 1
accelMDGRestart off
accelMDGcMDSteps 3000000
accelMDGEquiSteps 20000000
accelMDGcMDPrepSteps 200000
accelMDGEquiPrepSteps 200000
accelMDOutFreq 5000
accelMDGsigma0P 6.0
accelMDGsigma0D 6.0
accelMDGRestartFile pDMAEMA75_syn_opt3_out.restart.gamd

I was under the impression that when "accelMDGRestart off" is set,
NAMD uses the file name at
"accelMDGRestartFile pDMAEMA75_syn_opt3_out.restart.gamd" to create restart
files. However, NAMD never creates the file named
"pDMAEMA75_syn_opt3_out.restart.gamd", but it do create a restart file
appending $outputname.restart.gamd
my question is when namd restart files are created, does NAMD follow the
general procedure of writing restart files and append the ".restart.gamd"
for gamd related restart file?. And when we want to continue the
simulation, the corresponding restart file will be read into (in my case
"pDMAEMA75_syn_opt3_out.restart.gamd") through "accelMDGRestartFile"

I was a little confused about why,
accelMDGRestartFile pDMAEMA75_syn_opt3_out.restart.gamd
needed to be defined at step one since it does not require any gamd restart
Thank you,
Aravinda Munasinghe

Aravinda Munasinghe,

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