[gmx-users] energy conservation / frozen atoms
Justin Lemkul
jalemkul at vt.edu
Tue Jul 30 13:20:53 CEST 2013
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?
> 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.
-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
>
>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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