[gmx-users] Potential for Frozen atoms

[sukriti002]

mdp file:

; VARIOUS PREPROCESSING OPTIONS
title                    = 
cpp                      = /lib/cpp
include                  = 
define                   = -DPOSRES

; RUN CONTROL PARAMETERS
integrator               = l_bfgs
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.001
nsteps                   = 100000
; 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

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol                    = 10
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                  = 100
nstvout                  = 100
nstfout                  = 100
; Checkpointing helps you continue after crashes
nstcheckpoint            = 1000
; Output frequency for energies to log file and energy file
nstlog                   = 100
nstenergy                = 100
; Output frequency and precision for xtc file
nstxtcout                = 0
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 0
; ns algorithm (simple or grid)
ns-type                  = Grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc                      = no
; nblist cut-off        
rlist                    = 1.2
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = cutoff
rcoulomb                 = 1.2
; Method for doing Van der Waals
vdw-type                 = Switch
; cut-off lengths       
rvdw-switch              = 0
rvdw                     = 0.8
; Apply long range dispersi0n corrections for Energy and Pressure
DispCorr                 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 2
; 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               = 4e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel                  = no
gen-temp                 = 300
gen-seed                 = 173529

constraints = all-angles

freezegrps = V
freezedim = Y Y Y


Box is 3.5nm cube with no solvent. Cu2+ ions are 0.3 nm apart. Both sulphate
ions are 3nm away from from CU2+ ions. Cutoff distance is 1.2nm.

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