Thanks for the response. Yes, I know that large fluctuations will be expected. But why the average was not even correct? Also, how can I reach some state ( some pressre and temperature) and know/tell that the system is in equilibrium if the average is not correct with large fluctuation? I mean I do not know the criteria of Gromacs. Or maybe my procedure is wrong?
Message: 1 Date: Mon, 05 Jul 2010 10:39:30 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] pressure coupling To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4c31eea2.7070...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed Shuangxing Dai wrote: > Hi, all, > I am trying to do anisotropic coupling using Parrinello-Rahman. I > want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However, > I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, > fluctuation is 626 bar for pressure and 11.21 K for temperature.) I run > energy minimization first, then Berenderson pressure coupling for 50 ps, > finally Parrinello-Rahman pressure coupling for 50 ps. Anyone has > experience on anisotropic coupling and know why? > My system has just 4000 atoms. This is my .mdp file: > For a small system, large fluctations in the pressure are to be expected: http://www.gromacs.org/Documentation/Terminology/Pressure -Justin > ;define = -DPOSRES > ; RUN CONTROL PARAMETERS = > integrator = sd > ; start time and timestep in ps = > tinit = 0 > dt = 0.001 > nsteps = 50000 > ; number of steps for center of mass motion removal = > nstcomm = 100 > ; OUTPUT CONTROL OPTIONS = > ; Output frequency for coords (x), velocities (v) and forces (f) = > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Output frequency for energies to log file and energy file = > nstlog = 10 > nstenergy = 10 > ; Output frequency and precision for xtc file = > nstxtcout = 10 > xtc-precision = 1000 > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 20 > ; ns algorithm (simple or grid) = > ns_type = grid > > ;OPTIONS FOR PRESSURE COUPLING > Pcoupl = Parrinello-Rahman > pcoupltype = anisotropic > tau_p = 5 > compressibility = 2.1645e-07 2.1645e-07 2.7322e-07 0 0 0 > ref_p = 1 1 1 0 0 0 > ;OPTIONS FOR TEMPERATURE COUPLING > tc_grps = system > tau_t = 1 > ref_t = 1000 > ; OPTIONS FOR BONDS = > constraints = hbonds > ; Type of constraint algorithm = > constraint-algorithm = Lincs > ; Do not constrain the start configuration = > unconstrained-start = no > ; Relative tolerance of shake = > shake-tol = 0.0001 > ; Highest order in the expansion of the constraint coupling matrix = > lincs-order = 12 > ; Lincs will write a warning to the stderr if in one step a bond = > ; rotates over more degrees than = > lincs-warnangle = 30 > ; Periodic boundary conditions: xyz, no, xy > pbc = xyz > periodic_molecules = no > ; nblist cut-off > rlist = 1 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME > rcoulomb = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw = 1 > > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order = 6 > ewald_rtol = 1e-4 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > > > > I used the same procedure to reach different state ( like 0.01 K, 100K, > 300K, 500K, 800K, 1000K). Only the 0.01 K got the correct average > pressure and small fluctuation. > T p(bar) delta p T (K) delta T > 0.01 1.03E+00 2.12E+00 9.95E-03 1.21E-04 > 100 5.48359 71.5565 91.198 1.25218 > 300 2.62807 162.926 290.324 3.36594 > 500 16.6356 1048.76 492.616 5.45231 > 800 59.3245 594.773 799.314 9.18876 > 1000 80.2257 626.789 1007.23 11.2159 > > Thanks in advance, > Shuangxing Dai > Thanks, Shuangxing Dai
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