Re: GaMD in NAMD

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Thu Jun 14 2018 - 07:40:52 CDT

My protein is 25 kda.

Dhiraj

Sent from my iPhone

> On Jun 14, 2018, at 1:05 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> 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
>>
>> 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
>>>>
>>
>

This archive was generated by hypermail 2.1.6 : Fri Dec 06 2019 - 23:19:53 CST