[gmx-users] 1-4 interaction problem with a Thr
Aline Rossi
rossi.aline at gmail.com
Wed Oct 29 15:21:36 CET 2008
Sorry, I forgot to enclose the .mdp file:
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
title = PEP MD
cpp = /lib/cpp
constraints = none
integrator = md
tinit = 0
dt = 0.002 ; ps !
nsteps = 500000; total 1ns.
;mode for centre of mass motio removal
;comm-mode = linear
;number of steps for centre of mass motion removal
nstcomm = 1
nstxout = 5000;output coordinates every 0.5 ps
nstvout = 5000Íž output velocities every 0,5ps
nstlog = 5000
nstenergy = 250
nstxtcout = 250
xtc-precision = 1000
;Selection of energy groups
;NEIGHBORSEARCHING PARAMETERES
;nblist update frequency
nstlist = 10
;ns algorithm (simple or grid)
ns_type = grid
;nblist cut-off
rlist = 0.9
;domain-decomposition= no
;OPTIONS FOR ELECTROSTATICS AND VDW
;method for doing electrostatics
coulombtype = PME
rcoulomb = 0.9
;method for doing van der waals
rvdw = 0.9
;spacing for the PME FFT grid
fourierspacing = 0.12
;FFT grid size
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
;Ewald/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
constraint_algorithm = lincs
lincs_order = 4
;OPTIONS FOR WEAK COUPLING ALGORITHMS
; Berendsen temperature coupling is off in two groups
;TEMPERATURE COUPLING
Tcoupl = berendsen
tc-grps = Protein ISZ SOL NA+
tau_t = 0.1 0.1 0.1 0.1
ref_t = 310 310 310 310
;table-extension = 1.2
; Energy monitoring
;energygrps = Protein ISZ
; Isotropic pressure coupling is on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 310 K.
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
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