[gmx-users] Test Particle Insertion of Water

[Javier Cerezo]

What's your command line?

El 09/05/12 15:49, Steven Neumann escribió:
> title       = Test Particle Insertion
> ; Run parameters
> integrator  = tpi
> nsteps      = 50000000    ; 100 ns
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 0          ; suppress .trr output ; output coordinates 
> every 25 ps
> nstvout     = 25000     ; velocities to output every 25000 steps
> nstenergy   = 1000      ; save energies every 2 ps
> nstlog      = 1000      ; update log file every 2 ps
> nstxtcout   = 100000         ; suppress (tlumic) xtc trajectory
> energygrps  = System
> continuation    = no           ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds) 
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type     = grid      ; search neighboring grid cells
> nstlist     = 5         ; 10 fs
> vdwtype     = Switch
> rvdw-switch = 1.0
> rlist       = 1.4       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.4       ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.2       ; short-range van der Waals cutoff (in nm)
> ewald_rtol  = 1e-5      ; relative strenght of the Ewald-shifted 
> potential rcoulomb
> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.12      ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl      = V-rescale                     ; modified Berendsen 
> thermostat
> tc_grps     = System                 ; two coupling groups - more accurate
> tau_t       = 0.1                             ; time constant, in ps
> ref_t       = 318                         ; reference temperature, one 
> for each group, in K
> ; Pressure coupling is on
> pcoupl      = Parrinello-Rahman             ; pressure coupling is on 
> for NPT
> pcoupltype  = isotropic                     ; uniform scaling of box 
> vectors
> tau_p       = 2.0                           ; time constant, in ps
> ref_p       = 1.0                           ; reference pressure, in bar
> compressibility = 4.5e-5                    ; isothermal 
> compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = yes       ; assign velocities from Maxwell distribution
> gen_temp    = 318       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed

-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434