[gmx-users] Pressure Coupling in GROMACS

[Ebert Maximilian]

Hi Ashraf,

from the gromacs website (http://www.gromacs.org/Documentation/Terminology/Berendsen):

The distribution of temperatures and pressures (in the case of the thermostat and barostat, respectively) does not correspond to any known statistical mechanical ensemble.  It is best applied during the early stages of equilibration, as it converges relatively quickly and can be useful for stabilizing systems that may be far from equilibrium.

So you should ne use Berendsen for production only for equilibration. Check out one of those:

http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling

Max

On Jun 8, 2015, at 9:10 AM, Jashimuddin Ashraf <jashimuddin.ashraf23 at gmail.com<mailto:jashimuddin.ashraf23 at gmail.com>> wrote:

Dear GROMACS users,

I am new to GROMACS. My system contains only carbon nanotubes and inside my
md.mdp file I have-

----------------------------------------------------------------------------------------------------------------------------
.
.
Pcoupl                   = berendsen
Pcoupltype               = isotropic
tau_p                    = 1            ; @pressure coupling 1ps
compressibility          = 4.5e-5        ;
ref_p                    = 1.0            ; @reference pressure
.
.
----------------------------------------------------------------------------------------------------------------------------


whenever I run the grompp command, I get a warning called-


----------------------------------------------------------------------------------------------------------------------------

Using Berendsen pressure coupling invalidates the true ensemble for the
thermostat
----------------------------------------------------------------------------------------------------------------------------

I looked up at the mail list where I found Parrinello-Rahman to be
appropriate for the NPT simulations. But I intend to run production MD. Is
this an error to be
worried about? (I can obviously run simulations using maxwarn)

I have another problem. When I simulated carbon nanotubes with water/ other
molecules, the average pressure I observed from simulation (using g_energy
command) had a good agreement with the ref_p. But now the average pressure
becomes independent of my ref_p. This is a problem that is bugging me for a
long time. How can I resolve this?

Thanks in advance.
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