On 1/22/13 9:27 AM, Andrey Frolov wrote:
Dear Justin,
Considering all data points will include early frames that are not
necessarily
anywhere close to being equilibrated. You could try block averaging to see
if
the results converge to the correct result over the latter part of the
simulation, or at least see if the system is approaching the target
temperature.
Temperature jumps to the "wrong" target temperature at the beginning of the
simulation (see the figure attached). So, this is not the reason of the
problem.
<http://gromacs.5086.n6.nabble.com/file/n5004788/v-rescale_temperature_evolution.png>
It would be better to diagnose the system using PME. Even if the results
are
"similar," rounding errors are compounded when using plain cutoffs, which
render
the results inherently unreliable.
This is true. But, the problem persists even with PME. I have simulations
with slightly different setup: more CO2 molecules and higher CO2
concentration, umbrella windows for different separations between
paracetamol molecules, 24 ns simulation time, with PME electrostatics. Here
it gives me the "wrong" average temperature 478.486 K, while i set v-rescale
thermostat to 423.15 K. So, electrostatics method seems to play no role in
this.
Moreover, i tested the same simulation setups as in the initial posts with
Nose-Hoover thermostat. Single Nose-Hoover with number of chains = 1 gives
correct temperatures (the same as a set in mdp file). Even if i set three
thermostats to three subsystems (eventhough, i agree that this approach is
valid only for testing purposes) the resulting temperatures are correct.
But with N chains = 10, the resulting temperatures are again wrong (up to ~
20 K). (In this case integrator was md-vv).
As additional tests, can you set dt = 0.001 with the current setup, and then
also try constraining all bonds rather than just hbonds (with dt = 0.002)?
-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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