can you paste in your input file as text? I'm not sure of others on the
list, but I can't justify clicking on a link and downloading a zip file
just to see what might be going wrong in your simulation.
On Fri, Jun 16, 2017 at 10:26 AM, David Case <david.case.rutgers.edu> wrote:
> 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 - 08:00:02 PDT
