On Tue, Jul 30, 2013 at 7:04 AM, <gmx-users-requ...@gromacs.org> wrote:
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. generating user-defined topologies for surfaces (Valentina) > 2. Re: generating user-defined topologies for surfaces > (Justin Lemkul) > 3. Re: > energy conservation / frozen atoms (Justin Lemkul) > 4. Re: generating user-defined topologies for surfaces (Valentina) > 5. Re: generating user-defined topologies for surfaces (Valentina) > 6. Re: Re: generating user-defined topologies for surfaces > (Justin Lemkul) > > > > > ------------------------------ > > Message: 3 > Date: Tue, 30 Jul 2013 07:20:53 -0400 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] energy conservation / frozen atoms > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51f7a195.80...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 7/29/13 10:51 PM, S. Alireza Bagherzadeh wrote: > > Hi All, > > > > I am simulating a system in which I have two solid surfaces and I keep > them > > frozen during simulations. I also exclude the interactions between its > > atoms to avoid spurious contribution to the virial pressure due to large > > forces between them as suggested in the manual. > > > > I run a nvt for equilibration and then I do the production run in an nve > > ensemble; however, I am not getting good energy conservation. There is a > > huge energy drift... > > > > > > When I remove the solid surfaces, I will only have water molecules and > > united atom methane molecules in my system. Using the same protocol I > > obtain a very good energy conservation... > > > > What happens if you unfreeze the frozen surfaces and run the same system? > The point is I do not want to do this as I am trying to save some calculations. My system is already big and including all of the bond, angles and dihedral interactions of the solid surfaces slows down the simulation considerably. > > > Any insight on what might be wrong in my system would be very > appreciated. > > > > The contents of the .edr file will probably be informative, as you can > identify > which energy term(s) is(are) most affected. It's all probably related to > the > frozen surfaces themselves acting as an energy sink or something. > Is there anyway to fix the "energy sinking" effect of the surfaces? I used dl_poly to simulate a similar system and there was no problem with the energy conservation. Many thanks, Alireza > > -Justin > > > > > Here is the mdp file: > > > > ; > > ; File 'mdout_nve.mdp' was generated > > ; By user: onbekend (0) > > ; On host: onbekend > > ; At date: Sun Jul 28 18:13:02 2013 > > ; > > > > ; VARIOUS PREPROCESSING OPTIONS > > ; Preprocessor information: use cpp syntax. > > ; e.g.: -I/home/joe/doe -I/home/mary/roe > > include = > > ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case > sensitive) > > define = > > > > ; RUN CONTROL PARAMETERS > > integrator = md > > ; Start time and timestep in ps > > tinit = 0 > > dt = 0.001 > > nsteps = 1000000 > > ; For exact run continuation or redoing part of a run > > init_step = 0 > > ; Part index is updated automatically on checkpointing (keeps files > > separate) > > simulation_part = 1 > > ; mode for center of mass motion removal > > comm-mode = Linear > > ; number of steps for center of mass motion removal > > nstcomm = 100 > > ; group(s) for center of mass motion removal > > comm-grps = > > > > ; 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 = 0 > > nstvout = 0 > > nstfout = 0 > > ; Output frequency for energies to log file and energy file > > nstlog = 500 > > nstcalcenergy = -1 > > nstenergy = 500 > > ; Output frequency and precision for .xtc file > > nstxtcout = 0 > > 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 = HYDW HYDG SOL GAS SiO2 SiOH > > ; Selection of energy groups > > energygrps = HYDW HYDG SOL GAS SiO2 SiOH > > > > ; NEIGHBORSEARCHING PARAMETERS > > ; nblist update frequency > > nstlist = 10 > > ; ns algorithm (simple or grid) > > ns_type = grid > > ; Periodic boundary conditions: xyz, no, xy > > pbc = xyz > > periodic_molecules = no > > ; nblist cut-off > > rlist = 1.7 > > ; long-range cut-off for switched potentials > > rlistlong = -1 > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype = PME-Switch > > rcoulomb_switch = 1.3 > > rcoulomb = 1.5 > > ; Relative dielectric constant for the medium and the reaction field > > epsilon_r = 1 > > epsilon_rf = 1 > > ; Method for doing Van der Waals > > vdw-type = shift > > ; cut-off lengths > > rvdw-switch = 1.3 > > rvdw = 1.5 > > ; 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 = 6 > > ewald_rtol = 1e-06 > > ewald_geometry = 3d > > epsilon_surface = 0 > > optimize_fft = yes > > > > ; 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 = 1 > > ; 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 > > gb_dielectric_offset = 0.009 > > sa_algorithm = Ace-approximation > > ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of > GBSA > > ; The value -1 will set default value for Still/HCT/OBC GB-models. > > sa_surface_tension = -1 > > > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > > ; Temperature coupling > > tcoupl = no > > nsttcouple = -1 > > nh-chain-length = 1 > > ; Groups to couple separately > > tc_grps = system > > ; Time constant (ps) and reference temperature (K) > > tau_t = 0.2 > > ref_t = 370 > > ; Pressure coupling > > Pcoupl = no > > Pcoupltype = Isotropic > > nstpcouple = -1 > > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > > tau_p = 0.5 > > compressibility = 4.5e-05 > > ref_p = 40.0 > > ; 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 = no > > gen_temp = 370 > > gen_seed = -1 > > > > ; OPTIONS FOR BONDS > > constraints = none > > ; Type of constraint algorithm > > constraint-algorithm = shake > > ; 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 = 1e-10 > > ; Highest order in the expansion of the constraint coupling matrix > > lincs-order = 4 > > ; 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 = 1 > > ; 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 = SiOH SiOH SiO2 SiO2 SiOH SiO2 > > > > ; 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 = > > wall_density = > > wall_ewald_zfac = 3 > > > > ; 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 > > foreign_lambda = > > sc-alpha = 0 > > sc-power = 0 > > sc-sigma = 0.3 > > nstdhdl = 10 > > separate-dhdl-file = yes > > dhdl-derivatives = yes > > dh_hist_size = 0 > > dh_hist_spacing = 0.1 > > couple-moltype = > > couple-lambda0 = vdw-q > > couple-lambda1 = vdw-q > > couple-intramol = no > > > > ; Non-equilibrium MD stuff > > acc-grps = > > accelerate = > > freezegrps = SiO2 SiOH > > freezedim = Y Y Y Y Y Y > > 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 = > > > > ; User defined thingies > > user1-grps = > > user2-grps = > > userint1 = 0 > > userint2 = 0 > > userint3 = 0 > > userint4 = 0 > > userreal1 = 0 > > userreal2 = 0 > > userreal3 = 0 > > userreal4 = 0 > > > > > > > > > > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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