[gmx-users] 1-4 interaction problem with a Thr

[Aline Rossi]

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                  = 5000; 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