Re: GaMD in NAMD

From: Alexander Adams (xadams_at_umich.edu)
Date: Wed Jun 13 2018 - 23:15:12 CDT

Hi Dhiraj,

I've had success with the following parameters for dual-boosted GaMD:

accelMD on
accelMDdihe off
accelMDdual on
accelMDOutFreq 10
accelMDG on
accelMDGcMDPrepSteps 25000000 # steps before measuring energetics
for E and k0
accelMDGcMDSteps 50000000 # steps measuring energetics for
E and k0
accelMDGEquiPrepSteps 25000000 # steps with fixed E and k0 based
on cMD
accelMDGEquiSteps 100000000 # steps with E and k0 updated
each step
accelMDGRestart on
accelMDGRestartFile GaMD.gamd

I found these by consulting the following paper:
Gaussian Accelerated Molecular Dynamics in NAMD
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5743237/>

I believe this covers everything you are trying to specify if your
configuration, though it's not entirely clear.

Best of luck,
Alex Adams

On Wed, Jun 13, 2018 at 11:09 PM, Dhiraj Srivastava <dhirajks_at_gmail.com>
wrote:

> Hi Chitrak
> I am trying to use all the same parameter written on GaMD
> website but NAMD 2.13 is complaining about following parameters.
> ERROR: accelMDGrestfile
> ERROR: accelMDGntebprep
> ERROR: accelMDGntcmdprep
> ERROR: accelMDGnteb
> ERROR: accelMDGntcmd
> ERROR: accelMDGirest
>
> it don't recognize these parameters.
>
> Thanks
> Dhiraj
>
>
> On Wed, Jun 13, 2018 at 10:04 PM Chitrak Gupta <chgupta_at_mix.wvu.edu>
> wrote:
>
>> Hi Dhiraj,
>>
>> I have played around a bit with the NAMD implementation of GaMD. Which
>> parameters did you need help with?
>>
>>
>> Chitrak.
>>
>> On Wed, Jun 13, 2018 at 10:54 PM, Dhiraj Srivastava <dhirajks_at_gmail.com>
>> wrote:
>>
>>> Hi
>>> does anyone tried GaMD with NAMD? is theres any
>>> protocol/configuration file available? I am following the tutorial on
>>> https://gamd.ucsd.edu/tutorial_namd.html. however some of the
>>> parameters, NAMD can not understand.
>>>
>>> Thanks
>>> Dhiraj
>>>
>>
>>

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