[gmx-users] Pressure coupling and cut-off

Yanmei Song ysong30 at asu.edu
Fri May 15 00:54:10 CEST 2009

Dear All:

I have question about the pressure coupling. I have done a 10ns simulation
with 19800 atoms for 120 large molecules using the following pressure

Tcoupl              =  berendsen
tc_grps             =  PDM
tau_t               =  0.1
ref_t               =  300

Pcoupl              =  berendsen
pcoupltype          =  isotropic
;pc-grps            =  PDM
tau_p               =  1.0
ref_p               =  1.0
compressibility     =  4.5e-5

Then I did g_energy for the last 3ns and got the results:

Energy                      Average       RMSD     Fluct.      Drift
Potential                    -98061          0          0    0.61668
Temperature                 303.561    109.602    109.602 0.000181791
Pressure (bar)               4.4884    11110.8    11109.8  -0.169835

For such a long run the pressure drift is still too much and seem hasn't
approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did
a similar system by using the same method. it just take 2 or 3ns to reach
the equilibrium. and the pressure is around 1.01after the run. The only
difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4
is too large to make the system running slower. Or the pressure coupling
method is not working well.  Anyone can give me any suggestions?

Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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