Re: GaMD in NAMD

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jun 14 2018 - 01:05:52 CDT

How big was your system? As far as I know, recovering the real 3D energy
surface is only allowed for small systems.
francesco

On Thu, Jun 14, 2018 at 6:15 AM, Alexander Adams <xadams_at_umich.edu> wrote:

> 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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