[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

[xiaodong huang]

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?
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?
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).
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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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