On Fri, Jun 16, 2017, Ramin Salimi wrote:
>
> I heated up my system but I see the temperature increasing very sharply
> to 300k just in 1000 steps, which is weired to me for I have expected
> that increases linearly with the nmropt option. Why is that so? was my
> heating done correctly?
When interpreted correctly, the nmropt is programming the *target* temperature
profile. The relation of the actual temperature to the target temperature
depends upon the nature of the thermostat, and the assoicated parameters like
tautp or gamma_ln.
>
> It also starts at NSTEP=0 with TEMP=149.22. why? Is it not supposed to
> start at TEMP=100K?
This is a long-standing limitation of the way in which Amber randomizes
velocities. Run short simulations with ntpr=1, and follow the temperature.
It should go back to 100 (in this example) very quickly.
>
> #Explicit heating for 2ns although it heats up for the 1st ns only, then
> stabilizes for the other half.
I'm traveling right now, and can't look at this....maybe someone else on the
list can help out.
....dac
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Received on Fri Jun 16 2017 - 07:30:03 PDT
