[gmx-developers] pressure calculation in GROMACS CVS
David van der Spoel
spoel at xray.bmc.uu.se
Thu May 15 10:02:08 CEST 2008
Mareike Zink wrote:
> 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,
This is not consistent with the mdp file you sent, because there you
only have two T coupling groups. Here there are four in both cases, and
both look wrong. In 3.3.1 you have three groups with zero degrees of
freedom, and in the other one the last one is ridiculously large.
>
> 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
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> gmx-developers mailing list
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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