[gmx-developers] pressure calculation in GROMACS CVS
Berk Hess
hessb at mpip-mainz.mpg.de
Thu May 15 10:33:26 CEST 2008
Hi,
I was not sure if you tried the latest grompp, or only used the latest
mdrun.
But looking at your numbers, I would say that the CVS grompp is correct
and 3.3.1 grompp incorrect.
I checked the code where these numbers are calculated and I did not see
any differences
between 3.3.1 and CVS. I would like to know what caused this problem.
Could you somehow make the input files (top, gro, mdp, etc.) available
to me, via http or so?
I guess the system is too large to send via email.
This probably means that all your simulations with the tpr file
generated with your 3.3.1 grompp are incorrect.
Berk.
Mareike Zink wrote:
> David: The mdp file I sent was for my subsystem. Here is the mdp file for the
> complete simulation system with more than 4 mil. atoms.
>
> Berk: The temperature groups are
>
> Protein DAO ZN SOL_Na_Cl
>
> Group 1: Protein, 762,300 atoms
> Group 2: DAO: Fatty Acid, 2220 atoms
> Group 3: Zinc, 12 atoms
> Group 4: TIP4P water + Na + Cl ions: 3,451,758 atoms
>
> The pressure and volume values I sent you are from cvs version from April 15.
> Is there an even newer version? Then I can check (just needs some time
> because of the big system...)
>
>
> ;
> ; 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
>
>
>
>
>
> On Thursday 15 May 2008 10:01, you wrote:
>
>> 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,
>>>
>>> Mareike
>>>
>> This helps indeed.
>>
>> You seem to have three temperature coupling groups with zero degrees of
>> freedom.
>> What are these groups?
>>
>> There seems to be a bug in the CVS version of grompp that you used,
>> as the last group has 5 million degrees of freedom.
>>
>> Did you try the latest CVS version of grompp?
>> If not, could you do so and gmxcheck with 331?
>>
>> Berk.
>>
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