Yanmei Song wrote:
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 coupling.
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
Tot-Drift
-------------------------------------------------------------------------------
Potential -98061 0 0 0.61668
1850.04
Temperature 303.561 109.602 109.602 0.000181791
0.545372
Pressure (bar) 4.4884 11110.8 11109.8 -0.169835
-509.506
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?
I think it will depend on the interplay of other parameters as well. Posting a
complete .mdp file may be more helpful.
-Justin
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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