[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 23 05:25:08 CEST 2011
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?
Ideally, you'd get this distribution for a simple system, but the actual
distribution will be determined by how well the thermostatting algorithm
actually reproduces the expected behavior. You would have to consider
molecules, especially if you've used constraints.
> 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 all of these statistics; you do not need to assemble them
manually. Again, the distribution is only as good as the thermostatting algorithm.
> 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).
Read about your chosen barostat and how it is generally applied to such systems.
This will tell you what type of distribution might be expected. Pressure
values oscillate wildly in a simulation. Do not expect to get any sort of nice
distribution from them :)
http://www.gromacs.org/Documentation/Terminology/Pressure
> 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?
For an NPT ensemble, achieving the desired T and P (since v and T are not
independent, just as P and V are not) is the first step. As I've said, the
distributions depend on the algorithms and how faithfully they reproduce reality.
-Justin
> 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
> <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
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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