Well, the final average pressure is not correct: * **<====== ############### ==>* * **<==== A V E R A G E S ====>* * **<== ############### ======>* * * * Energies (kJ/mol)* * Buck.ham (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. * * 1.60633e+06 -5.69243e+06 -3.45003e+06 -7.53612e+06 1.80719e+04 * * Total Energy Temperature Pressure (bar)* * -7.51805e+06 3.62347e+02 1.11758e+04* * * * * * Pressure (bar)* * 1.21051e+04 -2.94017e-01 1.30456e+00* * -2.94017e-01 9.03597e+03 -8.10850e-01* * 1.30456e+00 -8.10850e-01 1.23863e+04* * * * * * **<====== ############################### ==>* * **<==== R M S - F L U C T U A T I O N S ====>* * **<== ############################### ======>* * * * Energies (kJ/mol)* * Buck.ham (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. * * 3.92376e+05 4.00326e+05 4.71365e+01 3.02978e+04 2.35039e+03 * * Total Energy Temperature Pressure (bar)* * 3.01091e+04 4.71259e+01 1.71117e+05* * * * * * Pressure (bar)* * 1.82323e+05 4.91513e+02 3.07107e+02* * 4.91513e+02 2.02402e+05 3.13857e+02* * 3.07107e+02 3.13857e+02 1.30179e+05* * * *Also the fluctuation is very large. I think 200ps is long enough. But still I cannot find the equilibrium.* *I do not know whether the parameters are wrong or I ran the anisotropic pressure coupling wrong. Is *Parrinello-Rahman pressure coupling sensitive to the initial pressure? I mean if the initial pressure ( in order of GPa), object pressure is 1 bar ( 1e5 Pa). * * Thanks, Shuangxing Dai
On Mon, Jun 14, 2010 at 8:50 PM, <gmx-users-requ...@gromacs.org> wrote: > > > Message: 3 > Date: Mon, 14 Jun 2010 19:18:14 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] anisotropic pressure coupling > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4c16b8b6.4010...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Shuangxing Dai wrote: > > Hi all: > > I was using Parrinello-Rahman for pressure coupling and here is the > > mdp file: > > > > ; RUN CONTROL PARAMETERS = > > integrator = sd > > ; start time and timestep in ps = > > tinit = 0 > > dt = 0.001 > > nsteps = 200000 > > ; number of steps for center of mass motion removal = > > nstcomm = 100 > > ; NEIGHBORSEARCHING PARAMETERS = > > ; nblist update frequency = > > nstlist = 50 > > ; ns algorithm (simple or grid) = > > ns_type = grid > > > > ;OPTIONS FOR PRESSURE COUPLING > > Pcoupl = Parrinello-Rahman > > pcoupltype = anisotropic > > tau_p = 1 > > compressibility = 2.1645e-09 2.1645e-09 2.7322e-09 0 0 0 > > ref_p = 1 1 1 0 0 0 > > ;OPTIONS FOR TEMPERATURE COUPLING > > tc_grps = system > > tau_t = 0.1 > > ref_t = 300 > > ; 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 > > > > It seems that the temperature coupling is fast and fluctuation is less > > that 1%. But the pressure coupling fails. The pressure fluctuates from > > +1e3 bar to -1e3 bar. Anyone can help? > > > > I don't call that failure. Depending on the size of your system, you can > probably expect very wide fluctuations in the pressure. Is the average > correct? > > http://www.gromacs.org/Documentation/Terminology/Pressure > > -Justin > > > > > Thanks, > > Shuangxing Dai > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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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