[gmx-users] pressure coupling questions

Erik Lindahl lindahl at csb.stanford.edu
Wed Oct 1 07:56:01 CEST 2003


First, NVT and NPT are well-defined ensembles, and not all 
pressure/temperature coupling methods reproduce them exactly. 
(Nose-Hoover for temperature and Parinello-Rahman for pressure).

"N" means constant number of particles.
"V" means constant volume (no pressure coupling) and "P" constant 
pressure (=coupling).
"T" means constant temperature and "E" constant energy (no temperature 

Now, you might be tempted to always use the well-defined ensemble 
coupling methods, but that's not always a good solution. The methods 
above (often called "extended ensemble") lead to larger fluctuations 
and can sometimes oscillate. For instance, if you want to simulate at 
constant pressure it is usually better to first run a short simulation 
(say 100ps) with berendsen pressure scaling which is guaranteed to 
converge rapidly. Then you just turn off the pressure scaling and keep 
the box constant during the rest of the run.

Gromacs reports pressure in bar. A negative pressure means the box 
would like to contract, i.e. your density is slightly too low. Pressure 
will fluctuate a lot in a microscopic system (thousands of bars), so 
you can't tell anything until you have an average over a couple of 
picoseconds. Even then,  -1000 isn't horribly off for a condensed phase 
system - your density will probably only change by a couple of percent 
if you enable pressure coupling.

Actually - as soon as you enable pressure coupling there will be a term 
in the energy file for the density (measured in SI units = kg/m3).



On Tuesday, September 30, 2003, at 07:17 AM, Q.Z. wrote:

> Dear All,
> I am new to md and gromacs. According to the manual and some the 
> tutorial, one can set either temp coupling or pressure coupling or 
> both at the same time. Does the temp coupling alone mean to use NVT 
> ensemble and pressure alone NPT ensemble? What is it when use both 
> coupling?
> If I turned off pressure coupling in my md but temp coupling on, I got 
> about average pressure of -1000 bar. What does that mean? Is the 
> density of my system too high? If it is, how should I change it?
> Thanks for any input.
> Q. Zou Ph D.
> Indiana Univ.
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