[gmx-users] Re: Anomaly in Temperature Behavior

Andrey Frolov andrey.i.frolov at mail.ru
Wed Jan 23 07:34:45 CET 2013

S. Alireza B wrote
> During this run we freeze the solid phase in
> all three dimensions. We then take the final configuration of this run,
> unfreeze the solid phase, and subject it to a long NVE simulation to study
> the dissociation of the solid phase...
> ... the temperature keeps increasing which is contrary to the physical
> fact that the dissociation
> process is endothermic.

1) Imagine you have just the solid state at the beginning of the simulation,
which is frozen (no forces are acting on the atoms). Then you unfreeze the
system, which means you switch on interactions between particles => non-zero
forces acting on particles appear. Despite the fact that the initial
velocities were zero, the non-zero forces in few integration time steps will
result in non-zero velocities on the particles, which means that temperature
will increase. So, to my mind, what you observe is not an anomaly. The solid
state in your NVE simulation is far from equilibrium. The quick increase of
temperature (in ~ 0.5 ps) is due to relaxation of the solid internal degrees
of freedom. I would expect, that no molecules melt to liquid phase in this
short time. Probably, you should just wait longer until solid starts melting

2) Also, I would suggest to prepare your system closer to equilibrium.
Instead of "freeze" you can use "position_restraints". Also, you can use
different  temperature coupling bathes to your solid and liquid. Setting
sufficiently lower reference temperature for the solid phase will prevent it
from melting.

3) Another suggestion, could it be that there is a spontaneous
crystallization in your system instead of melting ?

Andrey I. Frolov, PhD 
Postdoctoral fellow 
Institute of Solution Chemistry 
Russian Academy of Sciences 

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