[gmx-users] A question of Non-equilibrium MD in gromacs
陶璐
1049317895 at qq.com
Fri Jan 23 16:36:18 CET 2015
Hi all,
I'm running a MD simulation of water flowing between two layers of silicon. Now I'm trying to give a force in x direction on water molecules. But after the run, I found the velocity in the last .gro profile had no accelerations. Here attached the .mdp file. I have no idea where the bug exists. Your help is very appreciated.
Best,
TaoLu
; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /lib/cpp
include =
;define = -DPOSRES
;define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 1000000
;nsteps = 10
; 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
; Temperature, friction coefficient (amu/ps) and random seed
;bd-temp = 300
;bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 0.01
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/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 = 10000
nstvout = 10000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 10000
nstenergy = 10000
; Output frequency and precision for xtc file
nstxtcout = 0
xtc-precision = 10000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps = frez
; 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
periodic_molecules = yes
; nblist cut-off
rlist = 1
;periodic_molecules = no
;domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; 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 = v-rescale
; Groups to couple separately
tc-grps = UFF TOP SOL
; Time constant (ps) and reference temperature (K)
tau_t = 0.5 0.5 0.5
ref_t = 330 330 330
; Pressure coupling
Pcoupl = no
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 2.0 2.0
compressibility = 0.0 4.5e-5
ref_p = 0.0 10
; Random seed for Andersen thermostat
;andersen_seed = 815131
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = 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 = no
gen_temp = 330
gen_seed = 4773
; OPTIONS FOR BONDS
constraints = none
; 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 = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; 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) 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-sigma = 0.3
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl = frez frez
; Non-equilibrium MD stuff
acc-grps = SOL
accelerate = 0.1 0 0
freezegrps = frez
freezedim = Y Y Y
cos-acceleration = 0
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