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). Andrey -- View this message in context: http://gromacs.5086.n6.nabble.com/Temperature-coupling-problem-reference-T-is-different-to-given-T-in-mdp-file-tp5004780p5004788.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
