Hello world,
the following is my input file:
########
title = 2masn
cpp = /usr/bin/cpp
define = -DPOSRES
integrator = md
tinit = 0
dt = 0.002
nsteps = 1500000
init_step = 0
comm_mode = Angular
nstcomm = 1
comm_grps = Pore
nstxout = 250000
nstvout = 250000
nstfout = 250000
nstcheckpoint = 1000
nstlog = 2500
nstxtcout = 2500
xtc_grps = System
energygrps = Pore Membrane Ions Water
nstenergy = 2500
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.4
fourier_nx = 88
fourier_ny = 88
fourier_nz = 88
pme_order = 4
ewald_rtol = 1e-5
ewald_geometry = 3d
optimize_fft = yes
tcoupl = berendsen
tc_grps = Solute Solvent
tau_t = 0.1 0.4
ref_t = 300 300
pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 0.5 0.5 0.5 0.5 0.5 0.5
compressibility = 4.53e-5 4.53e-5 4.53e-5 0.0 0.0 0.0
ref_p = 1.025 1.025 1.025 1.025 1.025 1.025
gen_vel = yes
gen_temp = 300
gen_seed = 173529
constraints = all-bonds
constraint_algorithm = lincs
unconstrained_start = no
lincs_order = 4
lincs_iter = 2
lincs_warnangle = 30
################
and way after the very beginning of this simulation (~1.5ns) I always
get this error message:
##########
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.032676 17797 17799 0.003970
After LINCS 0.000004 17162 17169 0.000000
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
-------------------------------------------------------
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 1434. It should have been within [ 0 .. 1320 ]
Please report this to the mailing list (gmx-users@gromacs.org)
-------------------------------------------------------
#################
Is my input file so bad?
(I've seen people using lincs with 5fs time step...)
Thanks for any useful suggestion,
MG.
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