[gmx-users] bonds braking

[Eduardo Oliveira]

Hi,

I'm having trouble simulating a protein kinase on water. During the simulation, the molecule moves towards the box limits and some residues apear on the other side. Almost like they are interacting with water molecules on different sides of the box. I'm on my third simulation and the problem persists. I've already tried changing the periodic conditions but with no success. Waht are your thoughts on that?

For additional information:
Before the dynamics step I performed 4 minimization steps then i did water dynamics and the entire system dynamics.
Here is all the ".mdp " files.

Sorry in advance for the long email.

FIRST MINIMIZATION STEP:
title               =  min_steepest_descent_PR
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE -DPOSRES
constraints         =  none
integrator          =  steep ;l-bfgs
nsteps              =  20000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
pbc            =  xyz
coulombtype         =  PME 
rcoulomb            =  1.0
epsilon-r           =  1 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD
vdw-type            =  Cut-off
rvdw                =  1.4 ;     
emtol               =  209.2
emstep              =  0.01
fourierspacing        =  0.12
pme_order        =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes

SECOND MINIMIZATION STEP
title               =  min_steepest_descent
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
nsteps              =  20000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
pbc            =  xyz
coulombtype         =  PME
rcoulomb            =  1.0
epsilon-r           =  1.0 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD
vdw-type            =  Cut-off
rvdw                =  1.4
emtol               =  104.6
emstep              =  0.01
ewald_rtol          =  1e-5
optimize_fft        =  yes

THIRD MINIMIZATION STEP
title               =  min cg
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  cg
nsteps              =  20000
nstlist             =  10
ns_type             =  grid
nstcgsteep          =  100
rlist               =  1.0
pbc            =  xyz
coulombtype         =  PME
rcoulomb            =  1.0
vdw-type            =  Cut-off ;Switch
rvdw                =  1.4
emtol               =  41.84
emstep              =  0.01
ewald_rtol          =  1e-5
optimize_fft        =  yes

FOURTH MINIMIZATION STEP
title               =  min_steepest_descent
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  l-bfgs ;steep
nsteps              =  20000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
pbc            =  xyz
coulombtype         =  PME
rcoulomb            =  1.0
epsilon-r           =  1.0 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD
vdw-type            =  Cut-off
rvdw                =  1.4
emtol               =  41.84
emstep              =  0.01
ewald_rtol          =  1e-5
optimize_fft        =  yes

WATER DYNAMICS
title                    = 500ps_pr_fixo
cpp                      = /lib/cpp
define                   = -DPOSRES
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 250000 ; total 500 ps
comm-mode                = Linear
nstcomm                  = 1
nstxout                  = 500
nstvout                  = 20000
nstfout                  = 20000
nstlog                   = 1000
nstenergy                = 100
nstxtcout                = 500
xtc-precision            = 1000
energygrps               = Protein SOL NA 
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
domain-decomposition     = no
coulombtype              = PME
rcoulomb                 = 1.0
epsilon-r                = 1
vdw-type                 = Cut-off
rvdw                     = 1.4
DispCorr                 = EnerPres
optimize_fft             = yes
Tcoupl                   = V-rescale ;berendsen
tc-grps                  = Protein Non-protein   
tau-t                    = .1 .1 
ref-t                    = 310 310
gen_vel                  = yes
gen_temp                 = 310
gen_seed                 = 173529
Pcoupl                   = berendsen
Pcoupltype               = Isotropic
tau-p                    = 1
compressibility          = 4.5e-5
ref-p                    = 1
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = no
Shake-SOR                = no
shake-tol                = 1e-04
lincs-order              = 4
lincs-warnangle          = 30
morse                    = no

SYSTEM DYNAMICS
title                    = 10 ns
cpp                      = /lib/cpp
include                  = 
define                   = 
integrator               = md
tinit                    = 0 ;3000 ->continuar a partir de 3000 ps
dt                       = 0.002
nsteps                   = 5000000 ;500000 -> Mais 1ns de simulacao
comm-mode                = Linear
nstcomm                  = 1
nstxout                  = 50000 ; trr
nstvout                  = 50000 ; velocidades
nstfout                  = 50000 ; forcas
nstlog                   = 1000
nstenergy                = 100
nstxtcout                = 10000 ; xtc
xtc-precision            = 1000
energygrps               = Protein  SOL  NA        
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
domain-decomposition     = no
coulombtype              = PME
rcoulomb                 = 1.0
epsilon-r                = 1
vdw-type                 = Cut-off
rvdw                     = 1.4
DispCorr                 = EnerPres
optimize_fft             = yes
Tcoupl                   = V-rescale ;berendsen
tc-grps                  = Protein Non-protein     
tau-t                    = .1 .1         
ref-t                    = 310 310     
gen_vel                  = no
gen_temp                 = 310
gen_seed                 = 173529
Pcoupl                   = berendsen
Pcoupltype               = Isotropic
tau-p                    = 1
compressibility          = 4.5e-5
ref-p                    = 1
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = no
Shake-SOR                = no
shake-tol                = 1e-04
lincs-order              = 4
lincs-warnangle          = 30
morse                    = no