GROMACS version: 2020.2
GROMACS modification: No
I’m running a simulation of 1000 molecules of trichloroethylene. After an equilibration, which seems to have equilibrated well, I notice fast and large frequencies in the density (or volume) readings, which are related to the parameter ‘tau_p’ (this is the same tendency of the wave length).
I use the Parrinello-Rahman barostat. I tried to change the thermostat to the Nose-Hoover, change the compressibility, and adjust ‘tau_t’ and ‘tau_p’. However, I can’t avoid the oscillations.
Does anyone know how to solve this problem?
I’m attaching the mdp.
prod.mdp (910 Bytes)
Warning and Note:
“WARNING 1 [file topol.top, line 20]:
The following macros were defined in the ‘define’ mdp field with the -D
prefix, but were not used in the topology:
If you haven’t made a spelling error, either use the macro you defined,
or don’t define the macro.”
(I removed the POSRES.)
Cleaning up constraints and constant bonded interactions with virtual sites.
The number of degrees of freedom in the T-Coupling group System is 16,997.00.
NOTE 1 [file prod.mdp]:
There are 3000 non-linear virtual site constructions. Their contribution
to the energy error is approximated. In most cases, this does not affect
the error significantly.
(I’m not familiar with this note, as this is my first time using virtual atoms.)