On 8/19/12 7:39 AM, Shima Arasteh wrote:
Hi all,
In some simulations that I've studied, the "tcoupl"s chosen in nvt.mdp ,
npt.mdp or md.mdp are the same. Is it necessary to use the same temperature
coupling parameters in .mdp files? Generally, which parameters are supposed
to be the same in .mdp files of a simulation?
The thermostat can change. Generally, the Berendsen method is advisable for
initial NVT equilibration because it allows systems to relax gently. Starting
with Nose-Hoover, for instance, can lead to rapid instabilities and a crash.
Once equilibrated, a more rigorous method should be used.
Nearly all .mdp settings are identical for any phase of a simulation
(equilibration or data collection). Most of the settings are dictated by the
force field you've chosen, and since that's not changing, neither should your
.mdp settings. The thermostat might be adjusted, as stated above, and
restraints removed or applied, tau_t or tau_p may be adjusted as the system
reaches equilibrium. Outside of these settings, everything else is generally
static.
If a more accurate thermostat is used in a simulation, would it increase the
time of simulation? What kind of simulations worthwhile a more accurate
thermostats?
You should always use an accurate thermostat. Using a "better" thermostat does
not mean you have to run your simulation longer.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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