Re: GaMD in NAMD

From: David Hardy (
Date: Sun Jun 18 2017 - 11:02:19 CDT

Hi Chitrak,

This looks to me like a syntax problem in your config file.

If you haven't done so, you also need to specify "accelMD on" in your config file. Otherwise the accelMDG options will not activate.

Best regards,

David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
> On Jun 18, 2017, at 9:20 AM, Chitrak Gupta <> wrote:
> Hi Francesco,
> Thanks for your suggestion, I shall definitely get back to the paper. However, for now, I am trying to get the GaMD simulation run without an error. Would you know how to do that? I tried both NAMD 2.12 and the current nightly build version, both gave the following error in the log file
> Warning: The following variables were set in the
> Warning: configuration file but will be ignored:
> Warning:    accelMDdual (accelMD)
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR:    accelMDsigma0D
> ERROR:    accelMDSigma0P
> ERROR:    accelMDGEquiSteps
> ERROR:    accelMDGEquiPrepSteps
> ERROR:    accelMDGcMDSteps
> ERROR:    accelMDGcMDPrepSteps
> ERROR:    accelMDGRestart
> ERROR:    accelMDGiE
> ERROR:    accelMDG
> On Sun, Jun 18, 2017 at 2:04 AM, Francesco Pietra < <>> wrote:
> Be careful. Re-read the paper with GaMD implemented in NAMD, cheeking whether it could  potentailly solve your need, and compare with ABF and FEP (about which there is far more experience) before embarking in what could well later be disappointing (after huge amount of work)
> chiendarret 
> On Sat, Jun 17, 2017 at 10:16 PM, Chitrak Gupta < <>> wrote:
> Hello,
> I was wondering if anyone has worked with GaMD in NAMD 2.12 or the latest nightly build of NAMD. When I try it, all the GaMD options are ignored and the job crashes. Is there any tutorial on how to get this to work?
> Regards,
> Chitrak.

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