[gmx-users] Pressure problem: pressure is too large during MDsimulation

[Dallas B. Warren]

Plot the fluctuations of the pressure with time for the simulation.  Far
better way I think to get an idea of what is going on with a property
than just looking at values in a log file.  Especially when you are
starting out.

 

With pressure coupling, it is not unusual to have a fluctuation of a
hundred or so.  And that is nothing to worry about, entirely normal
behaviour to observe.  And with such large fluctuations, the average
pressure can deviate from the reference pressure.  Of course, with more
sample points and longer simulation time, it will get closer to the
reference value.

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Pan Wu
Sent: Monday, 12 October 2009 2:20 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Pressure problem: pressure is too large during
MDsimulation

 

Hi gmx users,

    I am now simulating one protein with solvent, in all atom
forcefield, gromacs official distributed version. The pressure of system
seems to be unreasonable large, and during the whole process, the box
keeps increasing.

    Here is how I set up the system,

    1. I solvate the proteini use spc216.gro, the log file shows: 

                 Output configuration contains 40990 atoms in 12386
residues

                 Volume: 412.593 (nm ^3)

                 Density: 1015.79 g/L
                 Number of SOL molecules: 13410

 

     2. Then I start to do MD with constrains (40 ps), then MD without
constrains.

                The md.log shows pressure keeps decrease, start from
5.79 e+02  until at last to about 3.14e+00, so you can see how large the
box size is enlarged.

         However in my setup, what I use for P-coupling is the same:

               Pcoupl = Berendsen

               Pcoupltype = isotropic

               tau_p = 0.5

               compressibility = 4.5e-5

               ref_p = 1.0

 

          my integral step size is 1fs, so the tau_p = 0.5 ps should be
enough. Also I checked the temperature, it is constant during the MD
process. (303K)

    

         So from these setup process, I think: the density is correct
for solvent water and system; the compressibility is chosen as for
standard water, the ref_p is chosen as 1.0. Why the pressure is so
large?

 

      Thank you in advance!
-- 
Sincerely
=================================
Pan Wu
Graduate Student in Department of Chemistry
Duke University
124 Science Drive
5301 French Family Science Center
Durham, NC 27708
Phone: (919) 660-1583
=================================

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