[gmx-users] Temperature and pressure coupling in the system with ice/water interface

Jun Soo Kim jskim9 at wisc.edu
Tue Nov 21 05:04:31 CET 2006


I have a system of ice and water mixture with the interface in the  
middle. I ran the MD simulation with Nose-Hoover T-coupling and  
Parrinello-Rahman P-coupling with constants 2ps for both of them to  
reproduce data of the recent publications.

The boxes of ice and water of TIP5P 768 molecules are prepared  
separately and combined along the Z direction. To remove the stress  
that may have been caused by combining them, the energy minimization  
was done and the short time MD simulation was also done.

For P-coupling, I used the semiisotropic coupling only in the  
direction of Z perpendicular to the interface, with XY fixed constant.

But unfortunately I get the large fluctuation in T and the weird  
pressure from 10ns simulation at the temperature below melting point  
as below. The fluctuation of T is always 3~5 irrespective tau_t used.  
and the average pressure is -80~-30 bar depending on the system size  
and the temperature.

Statistics over 10000001 steps [ 0.0000 thru 10000.0000 ps ], 2 data  

Energy                      Average       RMSD     Fluct.      Drift   
Temperature                     265    3.94956    3.94941  
1.20737e-05   0.120737
Pressure-(bar)             -33.3811    283.566    282.949   
0.0064756     64.756


I was wondering if this could just be ok or there could be something  
wrong with my .mdp file parameters. None of those literature used  
GROMACS didn't report the average and the error in their T and P.  
Only the literature, where their own MD code was used with Berendsen  
T and P coupling, reported T=268.1 +- 0.4K and P=1.3 +- 40atm with  
their target T=268K and P=1atm. Compared with this report, mine seems  
to be very inaccurate.

I am attaching a part of my .mdp file below.

Any comment would be appreciated. Thanks a lot in advance.

Sincerely Yours,
Jun Soo Kim

; Temperature coupling
Tcoupl                   = nose-hoover
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 2
ref_t                    = 260
; Pressure coupling
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 2 2
compressibility          = 0.0 4.5e-5
ref_p                    = 1.0 1.0
; Random seed for Andersen thermostat
andersen_seed            = 815131

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