[gmx-developers] pressure calculation in GROMACS CVS
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 14 22:57:20 CEST 2008
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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>>> gmx-developers at gromacs.org
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>>
>
>
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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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