[gmx-users] Re: Anomaly in Temperature Behavior

[S. Alireza Bagherzadeh]

Dear Andrey:


------------------------------
>
>
> S. Alireza B wrote
> > My concern is that at the end of my 0.5 ns NVT run the T is ~300K;
> > however,
> > at the first step of my NVE, when no forces has exerted on unfrozen
> > molecules yet, the T appears to be ~185K!
>
> Your explanation of this issue given in the first post sounds very
> meaningful. From general sense it is reasonable to consider the frozen
> particles just as sources of external potential field acting on the rest of
> the particles. So, one should not take into account frozen particles to
> calculate temperature of the system, what, i think, gromacs does.
>
> If you still have concerns, there is a way to figure it out of a simple
> test. E.g. generate a simulation system with two point particles. Freeze
> one
> particle, assign velocity to another one, evaluate temperature by mdrun,
> then unfreeze the first particle, check if it has a zero velocity, evaluate
> temperature by mdrun. If the temperature displayed by mdrun drops down in
> the second evaluation, then you were correct.
>

Thanks. I will test this. Unfortunately I have not got the chance yet...


>
>
> S. Alireza B wrote
> > The output configuration of my system shows that all of my solid phase
> has
> > melted. So, no crystallization occurred.
>
> Sorry, the output after 0.5 ps of simulation time in NVE shows complete
> melting?
>
> If it is true, that this illustrates that your crystal phase is really far
> from equilibrium with respect to internal degrees of freedom (has high
> potential energy). When you unfreeze this in your NVE simulation the
> potential energy tends to decrease, and the only way for it to decrease is
> to transform into kinetic energy (which increases), leading to increase of
> temperature.
>


It appears that my solid phase completely melts after 700 ps. Please see
the video below.
 http://www.youtube.com/watch?v=6iidpiivVRI&feature=youtu.be
Can I conclude that my solid phase is not really far from the equilibrium
as it does not suddenly melt/collapse?

-- 
S. Alireza Bagherzadeh
PhD Candidate
Dept. of Chem. & Bio. Eng.
University of BC
2360 East Mall
Vancouver BC V6T1Z3