Hey,

I'm running a 50 ns production simulation of a new CG peptide. During the production run all ions clump together in a string-like fashion then cluster together into large lumps in the system and around my peptide - is there a way I can stop this happening? They are NA and CL ions :)

Thanks!


Anna

Hey,

My peptide consists of Serine, Lysine, Glycine and Isoleucine beads :)

The bead types are in the .gro file here:
1GLY BB 1 5.500 5.970 8.457 0.0321 -0.1889 -0.1381
2ILE BB 2 5.539 6.248 8.433 -0.0441 0.1175 0.2417
2ILE SC1 3 5.291 6.428 8.382 0.0048 0.0187 -0.3530
3ILE BB 4 5.821 6.380 8.433 -0.5382 -0.0295 -0.2408
3ILE SC1 5 5.785 6.682 8.374 -0.1138 0.0255 -0.2124
4LYS BB 6 6.129 6.322 8.335 -0.4419 0.1299 0.1312
4LYS SC1 7 6.338 6.170 8.517 0.2437 -0.0474 -0.0635
4LYS SC2 8 6.401 5.981 8.708 0.0359 0.1261 0.1606
5SER BB 9 6.088 6.204 8.059 -0.1296 -0.0241 0.1312
5SER SC1 10 5.873 6.046 8.046 -0.2040 0.2811 0.1788
6ILE BB 11 6.413 6.154 7.931 -0.0365 0.0844 -0.0531
6ILE SC1 12 6.456 6.402 7.750 -0.0853 0.0600 -0.0976
7ILE BB 13 6.578 5.918 7.839 0.3101 0.1128 -0.0811
7ILE SC1 14 6.568 5.972 7.534 0.1234 -0.0627 -0.1056
8LYS BB 15 6.718 5.608 7.922 0.0321 0.0824 -0.1903
8LYS SC1 16 6.457 5.392 7.987 -0.0138 0.1463 -0.0142
8LYS SC2 17 6.332 5.296 8.139 0.0954 -0.1162 0.0266
9SER BB 18 6.992 5.441 7.970 -0.3956 0.3567 -0.2319
9SER SC1 19 6.961 5.203 7.877 0.0884 -0.0812 -0.0177
10ILE BB 20 7.279 5.491 8.193 0.1563 -0.2357 0.2483
10ILE SC1 21 7.486 5.322 8.037 -0.0443 -0.4676 0.2354
11ILE BB 22 7.386 5.781 8.482 0.1303 -0.1111 -0.3149
11ILE SC1 23 7.204 6.010 8.379 0.0793 -0.0047 0.0102
12LYS BB 24 7.265 5.625 8.796 0.0478 0.0462 -0.0177
12LYS SC1 25 7.082 5.399 8.693 0.2565 -0.0043 -0.2232
12LYS SC2 26 6.907 5.199 8.802 0.2128 0.2818 0.2625
13SER BB 27 7.105 5.634 9.109 -0.0574 -0.2658 -0.1664
13SER SC1 28 7.158 5.839 9.263 0.0154 0.1371 0.0659
14ILE BB 29 6.843 5.390 9.250 0.1102 0.0637 -0.1556
14ILE SC1 30 7.037 5.237 9.438 0.1397 0.1830 -0.0906

The .mdp out file is the example one suggested in the tutorials below:

define = -DPOSRES

; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 125000
; For exact run continuation or redoing part of a run
init-step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part = 1
; mode for center of mass motion removal
comm_mode = linear
; number of steps for center of mass motion removal
nstcomm = 100
; group(s) for center of mass motion removal
comm_grps = Protein W_NA+_CL-

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = -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 (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 5000
nstfout = 5000
; Output frequency for energies to log file and energy file
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
; Output frequency and precision for .xtc file
nstxout-compressed = 5000
compressed-x-precision = 1000
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps =
; Selection of energy groups
energygrps =

; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs)
cutoff-scheme = Verlet
; nblist update frequency
nstlist = 20
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
; nblist cut-off
rlist = 1.2
; long-range cut-off for switched potentials

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon-rf = 0
; Method for doing Van der Waals
vdwtype = Cut-off
vdw-modifier = Force-switch
; cut-off lengths
rvdw_switch = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Separate tables between energy group pairs
energygrp-table =
; 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-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
implicit-solvent = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = V-rescale
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc_grps = Protein W_NA+_CL-
; Time constant (ps) and reference temperature (K)
tau_t = 1.0 1.0
ref_t = 303.15 303.15
; pressure coupling
pcoupl = Berendsen
pcoupltype = Isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = com

; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme = normal
; QM basisset
QMbasis =
; QM charge
QMcharge =
; QM multiplicity
QMmult =
; Surface Hopping
SH =
; CAS space options
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
; Scale factor for MM charges
MMChargeScaleFactor = 1

; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; 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 = 300
gen-seed = -1

; OPTIONS FOR BONDS
constraints = h-bonds
; Type of constraint algorithm
constraint_algorithm = LINCS
; Do not constrain the start configuration
continuation = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; 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 =

; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype =
wall-density =
wall-ewald-zfac = 3

; COM PULLING
pull = no

; AWH biasing
awh = no

; ENFORCED ROTATION
; Enforced rotation: No or Yes
rotation = no

; Group to display and/or manipulate in interactive MD session
IMD-group =

; 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) and S to energy file
nstorireout = 100

; Free energy variables
free-energy = no
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
init-lambda = -1
init-lambda-state = -1
delta-lambda = 0
nstdhdl = 50
fep-lambdas =
mass-lambdas =
coul-lambdas =
vdw-lambdas =
bonded-lambdas =
restraint-lambdas =
temperature-lambdas =
calc-lambda-neighbors = 1
init-lambda-weights =
dhdl-print-energy = no
sc-alpha = 0
sc-power = 1
sc-r-power = 6
sc-sigma = 0.3
sc-coul = no
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1

; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =

; simulated tempering variables
simulated-tempering = no
simulated-tempering-scaling = geometric
sim-temp-low = 300
sim-temp-high = 300

; Ion/water position swapping for computational electrophysiology setups
; Swap positions along direction: no, X, Y, Z
swapcoords = no
adress = no

; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
; Electric fields
; Format for electric-field-x, etc. is: four real variables:
; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
; and sigma (ps) width of the pulse. Omega = 0 means static field,
; sigma = 0 means no pulse, leaving the field to be a cosine function.
electric-field-x = 0 0 0 0
electric-field-y = 0 0 0 0
electric-field-z = 0 0 0 0

; Density guided simulation
density-guided-simulation-active = false

Brilliant I see that now! Thanks so much for getting back to me!

Anna