[gmx-users] Re: Anomaly in Temperature Behavior

Andrey Frolov andrey.i.frolov at mail.ru
Mon Feb 4 09:07:24 CET 2013

S. Alireza B wrote
> 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?

Yes, i would conclude the same looking at this video. 

1) Do you still have the problem that the temperature keeps increasing (but
not decreasing) over the 700 ps  simulation ? If this is true, then it looks
strange to me. Then, i would think that the problem could with with the poor
energy conservation in the system. 

Such, gmx developers suggest to use PME-switch instead of PME. 
    A combination of PME and a switch function for the direct-space part
(see above). rcoulomb is allowed to be smaller than rlist. This is mainly
useful constant energy simulations.
Here, one should note that PME in gromacs is not exactly the same as in
other MD codes. In gromacs PME there is no cut-off for the real space Ewald
sum. But one could force it to do the cut-off with the switching function on
a tiny distance interval using "PME-Switch". Whether it improves the energy
conservation, i do not know.
In this discussion "http://redmine.gromacs.org/issues/196"  it is stated
that Gromacs PME "... can conserve energy better in single precision than
either Desmond, NAMD, Amber or Charmm do in double." Thus, to me it is not
clear why actually in the online manual it is suggested to use PME-Switch
for energy conservation. 

Anyway, i never did NVE simulations, so can not be much of help here. 

2) Comment 1: are you aware of "ewald_geometry = 3dc" ?  If you want to
simulate 2d periodic system (slab) in vacuum then this would be the correct
setup. If you want a 3d periodic system of infinite number of slabs, which
interact with each other, then the current setup is correct. 

3) Comment 2: you start your NVE simulation with zero velocities on the
molecules of solid phase (and, thus, zero temperature of the solid phase).
In this setup to melt the solid, one has to 1) heat the solid phase up to
its melting temperature and 2) melt it. Is it what you want to do ?


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