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

Dwey Kauffman mpi566 at gmail.com
Thu Sep 12 05:31:50 CEST 2013

Justin Lemkul wrote
> On 9/11/13 12:12 AM, Dwey Kauffman wrote:
>>> True, but thermostats allow temperatures to oscillate on the order of a
>>> few
>> K,
>>> and that doesn't happen on the macroscopic level either.  Hence the
>>> small
>>> disconnect between a system that has thousands of atoms and one that has
>>> millions or trillions.  Pressure fluctuations decrease on the order of
>> sqrt(N),
>>> so the system size itself is a determining factor for the pressure
>> fluctuations.
>>>   As previous discussions have rightly concluded, pressure is a somewhat
>>> ill-defined quantity in molecular systems like these.
>> Dose it also imply that it is not a good idea to study the relationship
>> between dimer (multimer) dissociation and  macroscopic pressure in this
>> case
>> ?  (due to the ill defined pressure).
> I would simply think it would be very hard to draw any meaningful
> conclusions if 
> they depend on a microscopic quantity that varies so strongly.
>> It is hard to be justified if I assign a set of various ref_p= 0.7, 0.8,
>> 0.9, 1.0, 1.1, 1.2 ...., perform independent simulations, and then obtain
>> outcomes of targeted quantities for comparison.
> As with the original issue, I would find it hard to believe that any of
> the 
> differences observed in such a setup would be meaningful.  Is 0.7 ± 100
> actually 
> different from 1.2 ± 100?
>>> You could try altering tau_p, but I doubt there is any value in doing
>>> so.
>> I would give it a try.
> This will really only change the relaxation time.  Smaller values of tau_p
> may 
> improve the average slightly, but may also (more likely) lead to
> instability, 
> especially with Parrinello-Rahman.

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.

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 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. 

Best regards,


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