[gmx-users] cool down problem
Riccardo Concu
ric.concu at gmail.com
Thu Oct 31 13:25:39 CET 2013
Dear all, I'm having some problems during the cool-down process after
the NVT.
I'm running the NVT process at a T of 500K for 3ns and everything is
going well but when I cool down the system blows up. I am running the
cool down for 100ps, I tried to run the process for longer time (500 ps)
and decrease nstlist option up to 5 but it seems it doesn't work. The EM
seems to be fine with very low forces:
Potential Energy = -3.1736706e+05
Maximum force = 2.6573439e+01 on atom 105
Norm of force = 3.1027287e-01
The NVT is compiled with the following mdp:
define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 1500000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 10000 ; save coordinates every 0.2 ps
nstvout = 10000 ; save velocities every 0.2 ps
nstenergy = 10000 ; save energies every 0.2 ps
nstlog = 10000 ; update log file every 0.2 ps
energygrps = NAP NA WAT MET SI3 SI- I LI+ LI-
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
vdwtype = cutoff
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
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
tcoupl = V-rescale ; modified Berendsen
thermostat
tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- ; two coupling
groups - more accurate
tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
0.1 ; time constant, in ps
ref_t = 500 500 500 500 500 500 500 500 500 ; reference
temperature, one for each group, in K
; Pressure coupling
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 298 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
The cooldown mdp is the following:
integrator = md
tinit = 0
dt = 0.001
nsteps = 100000; 100 ps
simulation_part = 1
init_step = 0
comm-mode = Linear
nstcomm = 1
comm-grps =
bd-fric = 0
ld-seed = 1993
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 500
nstenergy = 100
nstxtcout = 500
xtc-precision = 1000
xtc-grps =
nstlist = 10
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 0.9
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.9
epsilon_r = 1
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.0
DispCorr = No
table-extension = 1
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_epsilon_solvent = 80
gb_saltconc = 0
OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
Tcoupl = v-rescale
tc-grps = system
tau_t = 0.1
ref_t = 1000
Pcoupl = Parrinello-Rahman
Pcoupltype = Isotropic
tau_p = 2
compressibility = 4.5e-5
ref_p = 1
refcoord_scaling = No
andersen_seed = 815131
annealing = single
annealing_npoints = 2
annealing_time = 0 80
annealing_temp = 500 298
gen_vel = no
gen_temp = 500
gen_seed = 173529
constraints = all-bonds
constraint-algorithm = Lincs
continuation = no
iterations
Shake-SOR = no
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
morse = no
excluded
energygrp_excl =
nwall = 0
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
pull = no
disre = No
disre-weighting = Conservative
disre-mixed = no
disre-fc = 1000
disre-tau = 0
nstdisreout = 100
orire = no
orire-fc = 0
orire-tau = 0
orire-fitgrp =
nstorireout = 100
dihre = no
dihre-fc = 1000
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
Thank you all in advance,
Riccardo
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