From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Sun Jun 18 2017 - 14:57:20 CDT
Thanks Jeevan and David. I was indeed making the mistake of not switching
on "accelMD". That solved the problem.
Regards,
Chitrak.
On Sun, Jun 18, 2017 at 12:02 PM, David Hardy <dhardy_at_ks.uiuc.edu> wrote:
> 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,
> Dave
>
> --
> David J. Hardy, Ph.D.
> Theoretical and Computational Biophysics
> Beckman Institute, University of Illinois
> dhardy_at_ks.uiuc.edu
> http://www.ks.uiuc.edu/~dhardy/
>
>
> On Jun 18, 2017, at 9:20 AM, Chitrak Gupta <chgupta_at_mix.wvu.edu> 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 <chiendarret_at_gmail.com>
> 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 <chgupta_at_mix.wvu.edu>
>> 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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