[gmx-users] Decane layer
M.Naser
mn2 at hw.ac.uk
Fri Aug 5 16:19:32 CEST 2005
Hi All,
I have a decane box with 730 kg/m^3 and trying to run trial simulation but
crashing on me. It might be due to the bad contact. Is there any way I can
avoid that?
My mdp file as follows:
title = Decane
cpp = /lib/cpp
;define = -DPOSRES ; -DFLEX_SPC -DFLEXIBLE
;include = -I/home/bio/mn2/tutor/project1/
integrator = md
dt = 0.001
nsteps = 1000000
tint = 0
init_step = 0
comm_mode = linear
nstcomm = 1
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.9
vdwtype = switch
rvdw-switch = 0.8
rvdw = 0.9
fourierspacing = 0.1
pme_order = 4
ewald_rtol =1e-5
ewald_geometry =3dc
surface_epsilon =0
optimize_fft =yes
DispCorr = no
table-extension = 1
Tcoupl = Berendsen
tc_grps = system
tau_t = 0.1
ref_t = 300
Pcoupl = no
constraints = all-bonds
constraint_algorithm = shake ;lincs
unconstrained_start = no
shake_tol = 0.0001
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
Thanks in advance,
Abu
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