[gmx-users] RE: average pressure of a system

[Dallas Warren]

> I carried out independent NPT processes with different tau_p values =
> 1.5,
> 1.0 and 0.5
> 
> 
> 
> ## tau_p 1.5
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -----------------------------------------------------------------------
> --------
> Pressure                    2.62859        2.6     185.68    2.67572
> (bar)
> 
> 
> ## tau_p 1.0
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -----------------------------------------------------------------------
> --------
> Pressure                   0.886769        1.7    187.737      0.739
> (bar)
> 
> 
> 
> ## tau_p 0.5
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -----------------------------------------------------------------------
> --------
> Pressure                    2.39911        2.2    185.708     6.8189
> (bar)
> 
> ##############################
> 
> It is clear that when tau_p =1.0,  average pressure of the system
> (=0.89
> bar) is close to ref_p =1.0 bar
> However, it is unclear to me as to how to assign a good value to tau_p
> in
> order to reach at a close value of ref_p. As shown above, both of the
> average pressures  as  tau_p =1.5 and 0.5 are much higher than that as
> tau_p
> =1.0.  A smaller tau_p may or may not help.

As has been mentioned a number of times 0.9 +- 190 and 2.3 +- 190 are not statistically different.  If you use that in a publication then any conclusions based on that will be rejected.

To demonstrate to yourself how variable the pressure is, the tau_p=1 run, run the pressure analysis again using g_analyze, but using only the first half and the last half of the trajectory.  You will find that the average values for both parts of the trajectory are not the same.

> Another issue caused by system pressure  is about pbc box size. Since I
> use
> pressure coupling, the box size is not fixed such that protein moved
> away
> the center of membrane for a long simulation like 30 ns. Box size

That is not due to the pressure coupling.  Motion of the protein within the box is simply due to diffusion etc.  Also remember, that you have in effect an infinite repeating box in all directions, so the "center" of the box is arbitrary.  If you want the protein to remain in the center for visualisation purposes, then you do post processing on the box using trjconv.

> changes
> significantly during production MD. Is there a way to fix the box size
> at
> the very beginning ? although turning off pressure coupling will make
> box
> size fixed.

If you want fixed box dimensions / volume then you perform NVT.  But that will not help with either issues above.

The problem here is you are trying to make comparisons in the behaviour of simulations where there will not be a statistically significant difference in the property you are adjusting.  Any differences you observe are more than likely going to be due to chance, rather than pressure.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.