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

[xiaodong huang]

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?



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?

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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