Re: gamd restart file in namd 2.13

From: Pang, Yui Tik (
Date: Wed Dec 04 2019 - 09:55:30 CST

Hi Aravinda,

I am sorry the website was a bit confusing but no you do not need to set accelMDGRestartFile when accelMDGRestart is off. The GaMD restart file is indeed created following the general procedures of writing restart files and read in when accelMDGRestartFile is set and accelMDGRestart is on.

Andrew (Yui Tik Pang)
From: <> on behalf of Aravinda Munasinghe <>
Sent: Tuesday, December 3, 2019 9:17 AM
To: <>
Subject: namd-l: gamd restart file in namd 2.13

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" keyword?.

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 file.
Thank you,
Aravinda Munasinghe

Aravinda Munasinghe,

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