Re: GaMD in NAMD

From: Chitrak Gupta (
Date: Sun Jun 18 2017 - 09:20:11 CDT

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

On Sun, Jun 18, 2017 at 2:04 AM, Francesco Pietra <>

> 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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