GROMACS version:
GROMACS modification: Yes/No
Hi everybody,
I am trying to pull a gold nanoparticle toward a surface using an SMD simulation. However, from my trajectory, I noticed that in the initial frames of the simulation, the gold atoms appear to stretch in the z-direction (the pulling direction) and then reform into a sphere. However, the final configuration is no longer the original nanoparticle structure. Below is the code I am using. I would appreciate any suggestions on how to fix this issue.
title = OPLS Lysozyme NPT equilibration
; Run parameters
define = -DPOSRES
refcoord_scaling = No ; fix restraint
integrator = md ; leap-frog integrator
nsteps = 800000 ; 2 * 800000 = 1600 ps (1.6 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
nstxout-compressed = 500 ; save compressed coordinates every 1.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = C-rescale ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 0 ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
; Pull code
pull = yes
pull_ncoords = 1
pull_ngroups = 2
pull_group1_name = GNP_center
pull_group2_name = Surface
pull_coord1_type = umbrella
pull_coord1_geometry = distance
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes
pull_coord1_rate = -0.005
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2