[gmx-users] System

[s lal badshah]

Dear Justin,
Hi,
I want to do MD simulation of cholera toxin A-subunit.I took PDB file and remove other complexes from the protein so it comes to 185 amino acid residues.Through Whatif server I added the missing atoms. I uses oplsaa force field.Added about 11700 water molecules, closed it in cubic box, added 5 sodium ions.Run the energy minimization but it didn't reached the full and output says:Converged to machine precision, but not to the requested precision.The EM value was in negative.Then I do the equilibration and the mentioned errors occured.My EM file is:
title          = cholera.mdp
cpp            = /usr/bin/cpp ; the c preprocessor
include        = -I/usr/share/gromacs/top
define         = -DFLEXIBLE
constraints    = none
integrator     = steep
dt             = 0.002
nsteps         = 10000
nstlist        = 10
ns_type        = grid
rlist          = 1.0
coulombtype    = PME
rcoulomb       = 1.0
vdwtype        = cut-off
rvdw           = 1.4
fourierspacing = 0.12
fourier_nx     = 0
fourier_ny     = 0
fourier_nz     = 0
pme_order      = 4
ewald_rtol     = 1es
optimize_fft   = yes
;
;      Energy minimization stuff
emtol = 1000.0
emstep = 0.01
--------------------------------------------------------------------------------------------------
Wile pr.mdp file istitle           = pr.mdp
cpp             = /usr/bin/cpp
define          = -DPOSRES
constraints     = all-bonds
integrator      = md
dt              = 0.002
nsteps          = 100000
nstcomm         = 1
nstxout         = 250
nstvout         = 1000
nstlog          = 10
nstenergy       = 10
nstlist         = 10
ns_type         = grid
rlist           = 1.0
coulombtype     = PME
rcoulomb        = 1.0
vdwtype         = cut-off
rvdw            = 1.4
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e5
optimize_fft    = yes
;Berendsen temperature coupling is on
Tcoupl          = berendsen
tau_t           = 0.1       0.1 
tc-grps          = protein  non-protein
ref_t           = 298       298 
;Pressure coupling is on
Pcoupl          = berendsen
tau_p           = 20         20
compressibility = 4.5e-5     4.5e-5
ref_p           = 1.0        1.0
;Generate velocities is on at 298 K
gen_vel         = yes
gen_temp        = 298
gen_seed        = 173529
#############################################################
Waiting for your reply.
Regards,
Lal badshah.

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