[gmx-developers] pressure calculation in GROMACS CVS
Mareike Zink
mzink at gwdg.de
Thu May 15 09:45:16 CEST 2008
Hi,
I did gmxcheck and there is only one difference in the temperature groups,
nrdf:
gromacs 331.tpr
grpopts:
nrdf: 1.5144e+06 0 0 0
ref_t: 300 300 300 300
tau_t: 0.01 0.01 0.01 0.01
gromacs cvs.tpr
grpopts:
nrdf: 1.5144e+06 4500 36 5.18155e+06
ref_t: 300 300 300 300
tau_t: 0.01 0.01 0.01 0.01
All other options, coordinates, etc are completely identical.
Hope that helps,
Mareike
On Wednesday 14 May 2008 22:57, David van der Spoel wrote:
> mzink at gwdg.de wrote:
> > Hi Berk,
> >
> > here are the results from my complete simulation system. The simulations
> > were performed with CVS version from 2007-04-07. When preprocessing with
> > this version, the pressure is much too low and the volume changes
> > significantly during pressure scaling, resulting in a compression of my
> > protein (gyration radius declines by 0.2nm in the first steps, berendsen
> > tau_p=1ps):
> >
> > Time(ps) Volume
> > 0.000000 33352.519531
> > 1.000000 32016.798828
> > 2.000000 31509.839844
> > 3.000000 31247.882812
> > 4.000000 31129.593750
> > 5.000000 31069.384766
> >
> > Time(ps) Pressure
> > 0.000000 -1977.399414
> > 1.000000 -507.769196
> > 2.000000 -282.439423
> > 3.000000 -90.428642
> > 4.000000 -78.975014
> > 5.000000 -46.453594
> >
> > When I did grompp with the cvs version from 2007-06-21 or gromacs-331,
> > the pressure was about less then 100bar at step 0 and the box volume did
> > not change.
>
> So did you run, as Berk suggested, gmxcheck -s1 top33.tpr -s2 top40.tpr
> and look for differences?
>
> > Although the starting structure are identical, mdrun is always the same
> > and I checked tpr files with gmxcheck and gmxdump, I cannot find the
> > mistake. At the moment I have to perform the simulations with constant
> > volume or with cvs versions BEFORE july 2007, otherwise the box
> > compression destroys my system. Otherwise I have to run grompp with older
> > versions, than it is working with current cvs-mdrun. For me it seems so
> > that grompp is the problem and not mdrun but I don't have a clue what's
> > going on. Maybe you have an idea?
> >
> > Regards,
> > Mareike
> >
> >> Hi,
> >>
> >> The results you posted show, according to me, no significant difference
> >> in pressure and volume,
> >> except for the pressure at step 0.
> >>
> >> I assume, but you did not state this clearly, that both runs were done
> >> with exactly the same
> >> mdrun binary. I changed something with the constraining of the initial
> >> velocities in mdrun
> >> some time ago, which could explain the pressure difference at step 0.
> >> If it is really only a grompp version difference and not mdrun, I do not
> >> understand how this
> >> is possible.
> >>
> >> You can compare tpr files with:
> >> gmxcheck -s1 ... -s2 ...
> >>
> >> Berk.
> >>
> >> Mareike Zink wrote:
> >>> Dear GROMACS developers,
> >>>
> >>> I may found a bug in the pressure calculation of the current GROMACS
> >>> CVS version:
> >>>
> >>> My system (protein in water, approx. 320,000 particles) is equilibrated
> >>> in an
> >>> NPT ensemble and I want to run it with CVS version from 2007-07-04 or
> >>> the
> >>> current version from 2008-04-15 with a constant pressure of 1bar. The
> >>> following pressure and box volumes are given as an output:
> >>>
> >>> Time(ps) Pressure(bar)
> >>> 0.000000 1519.933594
> >>> 0.200000 1.404368
> >>> 0.400000 53.713745
> >>> 0.600000 -16.645607
> >>> 0.800000 -40.373356
> >>> 1.000000 64.932564
> >>>
> >>> Time(ps) Volume(nm³)
> >>> 0.000000 2458.407227
> >>> 0.200000 2458.920166
> >>> 0.400000 2458.617188
> >>> 0.600000 2459.025146
> >>> 0.800000 2459.828613
> >>> 1.000000 2459.592285
> >>>
> >>> When I did the preprocessing with a CVS version from 2007-06-21 or
> >>> GROMACS-3.3.1 but run the simulation with the CVS version from
> >>> 2007-07-04 or
> >>> 2008-04-15, the pressure and volume look much different:
> >>>
> >>> Time(ps) Pressure(bar)
> >>> 0.000000 95.616234
> >>> 0.200000 4.654475
> >>> 0.400000 59.303020
> >>> 0.600000 -7.656351
> >>> 0.800000 -1.787814
> >>> 1.000000 -9.527036
> >>>
> >>> Time(ps) Volume
> >>> 0.000000 2458.407227
> >>> 0.200000 2458.871582
> >>> 0.400000 2458.587158
> >>> 0.600000 2458.832031
> >>> 0.800000 2459.606445
> >>> 1.000000 2459.485107
> >>>
> >>>
> >>> Maybe there is a problem with the preprocessor. The problem with the
> >>> much too
> >>> high pressure only occures if grompp was done with a CVS version from
> >>> 2007-07-04 or later.
> >>>
> >>> Furthermore, the system I was using here, is just a subsystem of my
> >>> complete
> >>> simulation system which contains 4,5 Million atoms. Here I have the
> >>> same problem but the pressure is much too small (-2000bar). Due to the
> >>> wrong pressure, the pressure coupling rescales the box size within 1ps
> >>> (my tau_p)
> >>> and compresses the box to a much too small volume. Maybe the pressure
> >>> calculation is buggy?
> >>> Do you kno anything about this problem?
> >>>
> >>> My mdp-files for grompp with gromacs331 and cvs are below.
> >>>
> >>> If you need more information or files, please contact me.
> >>>
> >>> Thanx,
> >>>
> >>> Mareike
> >>>
> >>>
> >>> GROMACS 331:
> >>>
> >>> ;
> >>> ; File 'mdout.mdp' was generated
> >>> ; By user: mzink (37571)
> >>> ; On host: beany
> >>> ; At date: Mon Dec 18 12:45:54 2006
> >>> ;
> >>>
> >>> ; VARIOUS PREPROCESSING OPTIONS
> >>> title =
> >>> ; Preprocessor - specify a full path if necessary.
> >>> cpp = /lib/cpp
> >>> include =
> >>> define =
> >>>
> >>> ; RUN CONTROL PARAMETERS
> >>> integrator = md
> >>> ; Start time and timestep in ps
> >>> tinit = 0
> >>> dt = 0.002
> >>> nsteps = 5000
> >>> ; For exact run continuation or redoing part of a run
> >>> 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 =
> >>>
> >>> ; 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 = 0.000001
> >>> emstep = 0.01
> >>> ; Max number of iterations in relax_shells
> >>> niter = 100
> >>> ; Step size (ps^2) for minimization of flexible constraints
> >>> fcstep = 0
> >>> ; Frequency of steepest descents steps when doing CG
> >>> nstcgsteep = 1000
> >>> nbfgscorr = 10
> >>>
> >>> ; OUTPUT CONTROL OPTIONS
> >>> ; Output frequency for coords (x), velocities (v) and forces (f)
> >>> nstxout = 5000
> >>> nstvout = 5000
> >>> nstfout = 5000
> >>> ; Checkpointing helps you continue after crashes
> >>> nstcheckpoint = 5000
> >>> ; Output frequency for energies to log file and energy file
> >>> nstlog = 100
> >>> nstenergy = 100
> >>> ; Output frequency and precision for xtc file
> >>> nstxtcout = 500
> >>> 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 CA
> >>> ; Selection of energy groups
> >>> energygrps = Protein CA SOL
> >>>
> >>> ; NEIGHBORSEARCHING PARAMETERS
> >>> ; nblist update frequency
> >>> nstlist = 10
> >>> ; ns algorithm (simple or grid)
> >>> ns_type = grid
> >>> ; Periodic boundary conditions: xyz (default), no (vacuum)
> >>> ; or full (infinite systems only)
> >>> pbc = xyz
> >>> ; nblist cut-off
> >>> rlist = 0.9
> >>> domain-decomposition = no
> >>>
> >>> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >>> ; Method for doing electrostatics
> >>> coulombtype = PME
> >>> rcoulomb_switch = 0
> >>> rcoulomb = 0.9
> >>> ; Relative dielectric constant for the medium and the reaction field
> >>> epsilon_r = 1
> >>> epsilon_rf = 1
> >>> ; Method for doing Van der Waals
> >>> vdw-type = Cut-off
> >>> ; cut-off lengths
> >>> rvdw_switch = 0
> >>> rvdw = 0.9
> >>> ; Apply long range dispersion corrections for Energy and Pressure
> >>> DispCorr = No
> >>> ; 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 = 1e-05
> >>> ewald_geometry = 3d
> >>> epsilon_surface = 0
> >>> optimize_fft = 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
> >>> ; Salt concentration in M for Generalized Born models
> >>> gb_saltconc = 0
> >>>
> >>> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> >>> implicit_solvent = No
> >>>
> >>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> >>> ; Temperature coupling
> >>> Tcoupl = berendsen
> >>> ; Groups to couple separately
> >>> tc_grps = Protein Other
> >>> ; Time constant (ps) and reference temperature (K)
> >>> tau_t = 0.1 0.1
> >>> ref_t = 300 300
> >>> ; Pressure coupling
> >>> Pcoupl = berendsen
> >>> Pcoupltype = isotropic
> >>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> >>> tau_p = 1.0
> >>> compressibility = 4.5e-5
> >>> ref_p = 1.0
> >>> ; 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 = no no
> >>> ; 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 = 300
> >>> gen_seed = 173529
> >>>
> >>> ; OPTIONS FOR BONDS
> >>> constraints = all-bonds
> >>> ; Type of constraint algorithm
> >>> constraint-algorithm = Lincs
> >>> ; Do not constrain the start configuration
> >>> unconstrained_start = no
> >>> ; Use successive overrelaxation to reduce the number of shake
> >>> iterations Shake-SOR = no
> >>> ; Relative tolerance of shake
> >>> shake_tol = 1e-04
> >>> ; 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 =
> >>>
> >>> ; 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 = Equal
> >>> ; Use sqrt of the time averaged times the instantaneous violation
> >>> disre_mixed = no
> >>> disre_fc = 1000
> >>> disre_tau = 1.25
> >>> ; 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, Simple or Ensemble
> >>> dihre = No
> >>> dihre-fc = 1000
> >>> dihre-tau = 0
> >>> ; Output frequency for dihedral values to energy file
> >>> nstdihreout = 100
> >>>
> >>> ; Free energy control stuff
> >>> free_energy = no
> >>> init_lambda = 0
> >>> delta_lambda = 0
> >>> sc-alpha = 0
> >>> sc-power = 0
> >>> sc-sigma = 0.3
> >>>
> >>> ; 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 =
> >>>
> >>> ; User defined thingies
> >>> user1-grps =
> >>> user2-grps =
> >>> userint1 = 0
> >>> userint2 = 0
> >>> userint3 = 0
> >>> userint4 = 0
> >>> userreal1 = 0
> >>> userreal2 = 0
> >>> userreal3 = 0
> >>> userreal4 = 0
> >>>
> >>>
> >>> GROMACS CVS from 2007-04-07
> >>> ;
> >>> ; File 'mdout.mdp' was generated
> >>> ; By user: mzink (37571)
> >>> ; On host: beany
> >>> ; At date: Mon Mar 17 20:14:43 2008
> >>> ;
> >>>
> >>> ; VARIOUS PREPROCESSING OPTIONS
> >>> title =
> >>> ; Preprocessor - specify a full path if necessary.
> >>> cpp = /lib/cpp
> >>> include =
> >>> define =
> >>>
> >>> ; RUN CONTROL PARAMETERS
> >>> integrator = md
> >>> ; Start time and timestep in ps
> >>> tinit = 0
> >>> dt = 0.002
> >>> nsteps = 5000
> >>> ; For exact run continuation or redoing part of a run
> >>> 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 =
> >>>
> >>> ; 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 = 0.000001
> >>> emstep = 0.01
> >>> ; Max number of iterations in relax_shells
> >>> niter = 100
> >>> ; 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 = 5000
> >>> nstvout = 5000
> >>> nstfout = 5000
> >>> ; Checkpointing helps you continue after crashes
> >>> nstcheckpoint = 5000
> >>> ; Output frequency for energies to log file and energy file
> >>> nstlog = 100
> >>> nstenergy = 100
> >>> ; Output frequency and precision for xtc file
> >>> nstxtcout = 500
> >>> 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 CA
> >>> ; Selection of energy groups
> >>> energygrps = Protein CA SOL
> >>>
> >>> ; 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 = 0.9
> >>>
> >>> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >>> ; Method for doing electrostatics
> >>> coulombtype = PME
> >>> rcoulomb_switch = 0
> >>> rcoulomb = 0.9
> >>> ; Relative dielectric constant for the medium and the reaction field
> >>> epsilon_r = 1
> >>> epsilon_rf = 1
> >>> ; Method for doing Van der Waals
> >>> vdw-type = Cut-off
> >>> ; cut-off lengths
> >>> rvdw_switch = 0
> >>> rvdw = 0.9
> >>> ; Apply long range dispersion corrections for Energy and Pressure
> >>> DispCorr = No
> >>> ; 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 = 120
> >>> fourier_ny = 120
> >>> fourier_nz = 120
> >>> ; EWALD/PME/PPPM parameters
> >>> pme_order = 4
> >>> ewald_rtol = 1e-05
> >>> ewald_geometry = 3d
> >>> epsilon_surface = 0
> >>> optimize_fft = 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
> >>> ; Salt concentration in M for Generalized Born models
> >>> gb_saltconc = 0
> >>>
> >>> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> >>> implicit_solvent = No
> >>>
> >>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> >>> ; Temperature coupling
> >>> Tcoupl = berendsen
> >>> ; Groups to couple separately
> >>> tc_grps = Protein Other
> >>> ; Time constant (ps) and reference temperature (K)
> >>> tau_t = 0.1 0.1
> >>> ref_t = 300 300
> >>> ; Pressure coupling
> >>> Pcoupl = berendsen
> >>> Pcoupltype = isotropic
> >>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> >>> tau_p = 1.0
> >>> compressibility = 4.5e-5
> >>> ref_p = 1.0
> >>> ; 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 = no no
> >>> ; 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 = 300
> >>> gen_seed = 173529
> >>>
> >>> ; OPTIONS FOR BONDS
> >>> constraints = all-bonds
> >>> ; Type of constraint algorithm
> >>> constraint-algorithm = Lincs
> >>> ; Do not constrain the start configuration
> >>> continuation = yes
> >>> ; Use successive overrelaxation to reduce the number of shake
> >>> iterations Shake-SOR = no
> >>> ; Relative tolerance of shake
> >>> shake_tol = 1e-04
> >>> ; 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 =
> >>>
> >>> ; WALLS
> >>> ; Number of walls, type, atom types, densities and box-z scale factor
> >>> for
> >>> Ewald
> >>> nwall = 0
> >>> wall_type = 9-3
> >>> wall_atomtype =
> >>> wall_density =
> >>> wall_ewald_zfac = 3
> >>>
> >>> ; COM PULLING
> >>> ; Pull type: no, umbrella, constraint, 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 = Equal
> >>> ; Use sqrt of the time averaged times the instantaneous violation
> >>> disre_mixed = no
> >>> disre_fc = 1000
> >>> disre_tau = 1.25
> >>> ; 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, Simple or Ensemble
> >>> dihre = No
> >>> dihre-fc = 1000
> >>> dihre-tau = 0
> >>> ; Output frequency for dihedral values to energy file
> >>> nstdihreout = 100
> >>>
> >>> ; Free energy control stuff
> >>> free_energy = no
> >>> init_lambda = 0
> >>> delta_lambda = 0
> >>> sc-alpha = 0
> >>> sc-power = 0
> >>> sc-sigma = 0.3
> >>>
> >>> ; 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 =
> >>>
> >>> ; User defined thingies
> >>> user1-grps =
> >>> user2-grps =
> >>> userint1 = 0
> >>> userint2 = 0
> >>> userint3 = 0
> >>> userint4 = 0
> >>> userreal1 = 0
> >>> userreal2 = 0
> >>> userreal3 = 0
> >>> userreal4 = 0
> >>>
> >>>
> >>>
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