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

[Justin A. Lemkul]

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
> 

-- 
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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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