[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Jun 23 05:20:43 CEST 2011
On 23/06/2011 12:38 PM, xiaodong huang wrote:
> Dear Justin and gmxers
> Thank you so much for your helpful hints, but I am wondering how to
> check if I have
> obtained "proper distributions for the desired ensemble", as suggested
> in your email?
> My thoughts are:
> 1. As for NVT ensemble, I need to check if the velocity (or speed) of
> molecules in my simulation
> follows a Maxwell-boltzmann distribution, and the velocity is for
> the center of mass of these
> molecules, not for individual atoms, right?
Atoms are physical. Molecules are a convenient grouping of them to aid
human understanding.
> 2. Can I also check the distribution of T in my simulation (I output T
> every 100 steps or so, and
> make a statistics)? It is said in NVT ensemble, T follows a
> gaussian distribution, according
> to central limit theorem, and the square of its variance is
> 2T*T/(3N). Is that correct?
g_energy will report some descriptive statistics.
> 3. As for NPT ensemble, how to check if I have get a correction
> distribution from pressure
> coupling? Can I also check the P or V distribution? If so, what is
> the correct distribution I
> should get? I find some clues at "Understanding Modern Molecular
> Dynamics
> J. Phys. Chem. B 2000, 104, 159-178", but this paper just discuss
> some simple systems
> in T,P coupling section, and I still do not know the correct
> distribution I should
> get for my own simulations (e.g. protein in a box of water, NPT).
You need to use a small system that you can exhaustively sample, deduce
what the statistical distribution of your observables should be, and see
what you get. Or you can simply rely on the use of algorithms that have
been shown to produce correct distributions, and trust/verify that
GROMACS has implemented them correctly.
Mark
> 4.Are there any other quantities I need to check to make sure I have
> sampled a correct
> ensemble? I think to check the distribution of v, T, P V should be
> enough for this purpose,
> lthough to check more quantities is a plus, right?
> Any suggestions or comments are very welcome. Thank you.
> yours
> xiaodong
> Research School of Chemistry
> ANU
>
> On Tue, Jun 21, 2011 at 11:21 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> xiaodong huang wrote:
>
> Dear gromacs-ers
>
> I am using stochastic dynamics integrator (integrator = sd),
> so most of the time, I only need to adjust following
> parameters for temperature and pressure coupling: tau_t pcoupl
> tau_p (ref_t is room temperature and ref_p is 1 atm,
> compressibility can be taken from experimental numbers).
>
>
> In the manual, a tau_t between 1 and 2ps is recommended for
> the sake of simulation stability, but I see someone use a
> tau_t of 0.1ps with the same integrator (integration was
> performed with Langevin dynamics,49 with a reference
> temperature of 300 K and a weak frictional constant of 10
> ps-1,) when simulating water solvent. I also see someone use a
> tau_t of 0.2ps with the same integrator (To obtain a
> isothermal–isobaric ensemble at 293 K, a leap-frog stochastic
> dynamics integrator16 was used to integrate the equations of
> motion. The inverse friction constant was set to 0.2 ps.) when
> simulating some organic solvent. I check the references
> mentioned in these gromacs papers so I am pretty sure they are
> using the same integrator. So I am a bit confusing here, what
> tau_t should I use, the number between 1 and 2ps as
> recommended by the manual, or the numbers below 1ps, as
> reported in these papers? Does this parameter depend on what
> solvent (water, cyclohexane) I use? Can I just use any number
> between 0.1ps and 2ps and check if my simulations look fine or
> there is some ‘best’ number for a particular solvent?
>
>
> This was discussed recently:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-June/061992.html
>
>
>
> When I use berendsen or Parrinello-Rahman, the same questions
> apply: Is there some ‘best’ number for a particular solvent,
> or I can just use any number between 0.5ps and 5ps and check
> if my simulations run well?
>
>
> When I read papers, I find many different pressure coupling
> constant (tau_p) ranging from 0.5ps to 1ps (water), 1ps to 5ps
> (organic solvent) with weak coupling scheme in gromacs. I am
> wondering why they use bigger number for organic solvent? If I
> use Parrinello-Rahman (it is said to be better than berendsen
> in the manual), do I need to change tau_p, or I can just use
> the same tau_p as berendsen?
>
>
> Time constants are a bit empirical. The Berendsen algorithm is
> more forgiving; it relaxes very quickly and thus low values of
> tau_t/tau_p are stable. For methods that allow for wider
> oscillations (N-H for temperature, P-R for pressure), small
> tau_t/tau_p values are unstable due to the nature of these
> algorithms. The most important information is whether or not you
> obtain proper distributions for the desired ensemble. Any
> algorithm can be made to behave artificially rigorously or
> artificially relaxed.
>
> -Justin
>
>
> Thank you so much for your kind help, any suggestions or clues
> are very welcome.
>
> Yours
>
> xiaodong huang
> Research School of Chemistry
> ANU
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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