[gmx-developers] pressure calculation in GROMACS CVS
Mareike Zink
mzink at gwdg.de
Thu May 15 10:21:05 CEST 2008
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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