So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization but I still can't get my large system to work with pressure coupling. I tried minimizing but I can never get the Fmax to be less 10^2, which is pretty normal for protein/water simulations of large proteins, at least from my experience. I have since run 400 ps NVT as the system (425K atoms) is quite stable. The <P.E.> is 2E-05. Since I am using 4fs time steps gromacs won't let me use a tau_p less than .4. Not sure what else to do except run NVT, which is what I was going to do after I got the density equilibrated. BTW, I am using octahedral PBC, but that should not make a difference with respect to P coupling, should it? Below is my whole mdp file. As a reminder my density in the system goes from 1.0 - .1 in 10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the amount of time it takes for my system to expand increases but it still expands. ; ; File 'mdout.mdp' was generated ; By user: relly (508) ; On host: master.simprota.com ; At date: Fri Mar 6 20:17:33 2009 ;
; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.004 ;nsteps = 250000 nsteps = 2500000 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step = 0 ; mode for center of mass motion removal comm_mode = linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm_grps = system ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 10 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 12500 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 = 250 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = protein ; Selection of energy groups energygrps = Protein SOL ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist = 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = .9 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon-r = 80 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = .8 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; 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 = 4 ewald_rtol = 1.e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = V-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 1.0 ref_t = 298.0 ; Pressure coupling Pcoupl = No Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 10 compressibility = 4.5e-5 ref_p = 1.01325 ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed = 815131 ; OPTIONS FOR QMMM calculations QMMM = no ; Groups treated Quantum Mechanically QMMM-grps = ; QM method QMmethod = ; QMMM scheme QMMMscheme = normal ; QM basisset QMbasis = ; QM charge QMcharge = ; QM multiplicity QMmult = ; Surface Hopping SH = ; CAS space options CASorbitals = CASelectrons = SAon = SAoff = SAsteps = ; Scale factor for MM charges MMChargeScaleFactor = 1 ; Optimization of QM subsystem bOPT = bTS = ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 298.0 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 6 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 2 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall = 0 wall_type = 9-3 wall_r_linpot = -1 wall_atomtype = ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = no ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) and S to energy file nstorireout = 100 ; Dihedral angle restraints: No or Yes dihre = no dihre-fc = 1000 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 deform = ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = E-xt = E-y = E-yt = E-z = E-zt = On Wed, Apr 8, 2009 at 1:00 PM, Joe Joe <ilcho...@gmail.com> wrote: > > > On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz <rol...@utk.edu> wrote: > >> >> >> On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe <ilcho...@gmail.com> wrote: >> >>> HI Chris, >>> >>> On Tue, Apr 7, 2009 at 9:31 PM, <chris.ne...@utoronto.ca> wrote: >>> >>>> Hi Ilya, >>>> >>>> First thing that comes to mind is that it is strange to couple a >>>> coulombic switching function with PME. While this could possibly be done >>>> correctly, I doubt that it is in fact done in the way that you expect (i.e. >>>> correctly) in gromacs. In fact, I think that grompp/mdrun should probably >>>> throw an error here -- unless it is actually handled in the proper way, and >>>> a developer could help you here to figure out if you are indeed getting >>>> what >>>> you desire. >>>> >>>> coulombtype = PME >>>> rcoulomb-switch = .9 >>>> rcoulomb = 1.0 >>> >>> >>> I am pretty sure gromacs ignores the rcoulomb-switch parameter in the >>> case of PME but I will give it a try. >>> >> >> It is indeed supported and does work correctly. But you have to set >> coulombtype PME-Switch. mdp options says: >> "This is mainly useful constant energy simulations. For constant >> temperature simulations the advantage of improved energy conservation is >> usually outweighed by the small loss in accuracy of the electrostatics. " >> >> Roland >> > > Yes, my point was that when electrostatics = PME then Gromacs ignores the > rcoulomb-switch parameter. > >> >> >> >>> >>>> >>>> Chris >>>> >>>> -- original message -- >>>> >>>> Hi >>>> I am having some pressure coupling issues. I have a fairly large >>>> protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If >>>> I >>>> run NVE it conserves energy with appropriate parameter settings. If I >>>> run >>>> NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello >>>> Rahman), the system just continuously expands. My parameters are as >>>> follows. >>>> Any ideas? >>>> >>>> Best, >>>> >>>> Ilya >>>> >>>> ; >>>> ; File 'mdout.mdp' was generated >>>> ; By user: relly (508) >>>> ; On host: master.simprota.com >>>> ; At date: Fri Mar 6 20:17:33 2009 >>>> ; >>>> >>>> ; VARIOUS PREPROCESSING OPTIONS >>>> ; Preprocessor information: use cpp syntax. >>>> ; e.g.: -I/home/joe/doe -I/home/mary/hoe >>>> include = >>>> ; e.g.: -DI_Want_Cookies -DMe_Too >>>> define = >>>> >>>> ; RUN CONTROL PARAMETERS >>>> integrator = md >>>> ; Start time and timestep in ps >>>> tinit = 0 >>>> dt = 0.004 >>>> ;nsteps = 250000 >>>> nsteps = 2500000 >>>> ; For exact run continuation or redoing part of a run >>>> ; Part index is updated automatically on checkpointing (keeps files >>>> separate) >>>> simulation_part = 1 >>>> init_step = 0 >>>> ; mode for center of mass motion removal >>>> comm_mode = linear >>>> ; number of steps for center of mass motion removal >>>> nstcomm = 1 >>>> ; group(s) for center of mass motion removal >>>> comm_grps = system >>>> >>>> ; 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 = 250 >>>> xtc-precision = 1000 >>>> ; This selects the subset of atoms for the xtc file. You can >>>> ; select multiple groups. By default all atoms will be written. >>>> xtc-grps = protein >>>> ; Selection of energy groups >>>> energygrps = >>>> >>>> ; NEIGHBORSEARCHING PARAMETERS >>>> ; nblist update frequency >>>> nstlist = 5 >>>> ; ns algorithm (simple or grid) >>>> ns_type = grid >>>> ; Periodic boundary conditions: xyz, no, xy >>>> pbc = xyz >>>> periodic_molecules = no >>>> ; nblist cut-off >>>> rlist = 1.0 >>>> >>>> ; OPTIONS FOR ELECTROSTATICS AND VDW >>>> ; Method for doing electrostatics >>>> coulombtype = PME >>>> rcoulomb-switch = .9 >>>> rcoulomb = 1.0 >>>> ; Relative dielectric constant for the medium and the reaction field >>>> epsilon-r = 80 >>>> epsilon_rf = 1 >>>> ; Method for doing Van der Waals >>>> vdw-type = Switch >>>> ; cut-off lengths >>>> rvdw-switch = .9 >>>> rvdw = 1.0 >>>> ; Apply long range dispersion corrections for Energy and Pressure >>>> DispCorr = EnerPres >>>> ; Extension of the potential lookup tables beyond the cut-off >>>> table-extension = 1 >>>> ; Seperate tables between energy group pairs >>>> energygrp_table = >>>> ; 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 = 4 >>>> ewald_rtol = 1.e-05 >>>> ewald_geometry = 3d >>>> epsilon_surface = 0 >>>> optimize_fft = no >>>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS >>>> ; Temperature coupling >>>> Tcoupl = V-rescale >>>> ; Groups to couple separately >>>> tc-grps = System >>>> ; Time constant (ps) and reference temperature (K) >>>> tau_t = 0.1 >>>> ref_t = 298.0 >>>> ; Pressure coupling >>>> Pcoupl = Berendsen >>>> Pcoupltype = Isotropic >>>> ; Time constant (ps), compressibility (1/bar) and reference P (bar) >>>> tau_p = 10 >>>> compressibility = 4.5e-5 >>>> ref_p = 1.01325 >>>> ; Scaling of reference coordinates, No, All or COM >>>> refcoord_scaling = No >>>> ; Random seed for Andersen thermostat >>>> andersen_seed = 815131 >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> Please don't post (un)subscribe requests to the list. Use thewww >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> >> -- >> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov >> 865-241-1537, ORNL PO BOX 2008 MS6309 >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
