[gmx-users] Re: Langevin thermostat implementation in GROMACS vs AMBER
Christoph Junghans
junghans at votca.org
Wed May 8 19:33:51 CEST 2013
> Date: Wed, 08 May 2013 16:34:46 +0200
> From: Julian Garrec <julian.garrec at epfl.ch>
> Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS
> vs AMBER
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <518A6286.8020504 at epfl.ch>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> No suggestion ?? :)
>
> In my post I forgot to say that my system contains explicit water.
>
> I'm still very curious about the difference in implementation in AMBER
> and GROMACS. And I still don't really understand the meanning of tau-t
> in LD and how it is related to other (well defined) quantities such as
> the friction coeficient in equation 3.114 of the manual (v4.6.1).
I am not really sure what your question is, section 7.3.3 is pretty
clear about that:
"the inverse friction constant for each group is set with tau-t", so
gamma_i=1/tau-t, which also makes sense unit-wise as gamma has units
1/ps and tau-t ps
bd-fric is only used for the Brownian dynamics integrator and if
bd-fric=0, the friction is calculated as mass/tau-t. It might be a bit
misleading that bd-fric is listed under section 7.3.4 (Langevin
dynamics), but that stems from the fact that Brownian dynamics is the
overdamped case of stochastic dynamics and hence it is Langevin
Dynamics, too, just in a different limit.
Christoph
>
> Please help,
>
> Sincerely,
>
> Julian
>
>
> Le 04/05/13 13:42, Julian Garrec a 閏rit :
>> Dear all,
>>
>> I am trying to use stochastic dynamics in GROMACS to reproduce some
>> previous results that I got with the AMBER software using the Langevin
>> thermostat.
>>
>> In AMBER, one typically sets what they call the "collision frequency"
>> (noted gamma_ln in the AMBER manual). I typically set gamma_ln to 2
>> collisions per ps (significantly smaller than the internal friction of
>> water, since I use Langevin dynamics as a thermostat).
>>
>> 1) In the mdp options manual, it is recommended to use {integrator=sd
>> ; bd-fric=0 ; tau-t=2}. My understanding is that bd-fric corresponds
>> to 'm_i*gamma_i' in equation 3.114 of the theoretical part of the
>> manual (version 4.6.1). Am I right ?
>>
>> 2) Then, is {integrator=sd ; bd-fric=0 ; tau-t=2} equivalent to
>> {integrator=sd ; bd-fric=0.5} ? (In the theoretical part of the
>> manual, it is said that gamma_i should be set to 0.5 to follow the
>> same spirit).
>>
>> 3) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ?
>>
>> Thanks for your help,
>>
>> Julian
>>
>
>
> --
> Julian Garrec, research associate
>
> Web: https://sites.google.com/site/juliangarrec/
>
> 蓂uipe : Chimie et Biochimie Th閛riques
> Unit�Mixte de Recherches CNRS UHP 7565
> Universit�de Lorraine, Nancy I BP 239,
> 54506 Vandoeuvre-l鑣-Nancy, cedex France
--
Christoph Junghans
Web: http://www.compphys.de
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