[gmx-developers] pressure calculation in GROMACS CVS

Berk Hess hessb at mpip-mainz.mpg.de
Thu May 15 10:57:07 CEST 2008


Hi,

The mdp file below has only 2 temperature coupling groups.
Could you mail the correct mdp file?

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
>
>
>
>
>
>   




More information about the gromacs.org_gmx-developers mailing list