[gmx-users] A question of Non-equilibrium MD in gromacs

[陶璐]

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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