[gmx-users] system is bigger but box remains

[taveechai taveecharoenkool]

dear all,
 i have  a system of six protein-monomers in popc
bilayers, there is a pore inside this hexamers. i want
to study the free energy difference of K in the pore
between mutant and wild-type of this hexamer. i put K
at center of the pore 0 0 0. Then , perform energy
minimization by steepest descent, and cg. However,
after energy minimization , the system is bigger , the
box vector the same . Then i look at the structure by
RasMol the system looks weird. the pore doesn't appear
, the proteins went to the corners of the box,
bilayers of popc also disappear, water in the middle
of popc layer. i remove pbc out using ' editconf -pbc
' , but the system still look the same. 
please help me , i just want to get K ion in the local
minimum of this pore.
 system size : 13.360 16.203 14.029 (nm)
    center      :  5.301  5.903  5.029 (nm)
    box vectors : 10.803 11.910 11.177 (nm)
this is mdp file:
; VARIOUS PREPROCESSING OPTIONS =
title                    =
cpp                      = /lib/cpp
include                  =
define                   =

; RUN CONTROL PARAMETERS =
integrator               = steep
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.0002
nsteps                   = 50000
;                        = 100 ps REMARK  
; number of steps for center of mass motion removal =
nstcomm                  = 1
         
; LANGEVIN DYNAMICS OPTIONS = 
; Temperature, friction coefficient (amu/ps) and
random seed =
bd-temp                  = 300 
bd-fric                  = 0
ld-seed                  = 1993
    
; ENERGY MINIMIZATION OPTIONS = 
; Force tolerance and initial step-size =
emtol                    = 1
emstep                   = 0.01
; Max number of iterations in relax_shells = 
niter                    = 0
; Frequency of steepest descents steps when doing CG =

nstcgsteep               = 1000
; OUTPUT CONTROL OPTIONS = 
; Output frequency for coords (x), velocities (v) and
forces (f) =
nstxout                  = 1000
nstvout                  = 1000
nstfout                  = 0
; Output frequency for energies to log file and energy
file =
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file =
nstxtcout                = 1000
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file.
You can =
; select multiple groups. By default all atoms will be
written. =
xtc-grps                 =
; Selection of energy groups =
energygrps               = Protein POPC SOL K

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 15
; ns algorithm (simple or grid) =
ns-type                  = Grid
; Box type, rectangular, triclinic, none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.0
domain-decomposition     = no
 OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 1.0
; Dielectric constant (DC) for cut-off or DC of
reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = Cut-off
; cut-off lengths        =
rvdw-switch              = 0
rvdw                     = 1.0
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.15
; FFT grid size, when a value is 0 fourierspacing will
be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
optimize_fft             = yes

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = yes
; Groups to couple separately =
tc-grps                  = Protein POPC SOL K
tau-t                    = 0.1 0.1 0.1 0.1
ref-t                    =  300 300 300 300
; Pressure coupling      =
Pcoupl                   = berendsen
Pcoupltype               = Anisotropic
; Time constant (ps), compressibility (1/bar) and
reference P (bar) =
tau-p                    = 1.0
compressibility          = 4.5E-5 4.5E-5 4.5E-5 4.5E-5
4.5E-5 4.5E-5
ref-p                    = 1.0 1.0 1.0 1.0 1.0 1.0

; SIMULATED ANNEALING CONTROL =
; annealing                = no
; Time at which temperature should be zero (ps) =
; zero-temp_time           = 0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen-vel                  = yes
gen-temp                 = 300
gen-seed                 = 173529

; OPTIONS FOR BONDS     =
constraints              = all-bonds
; Type of constraint algorithm =
constraint-algorithm     = Lincs
; Do not constrain the start configuration =
unconstrained-start      = no
; Relative tolerance of shake =
shake-tol                = 0.0001
; Highest order in the expansion of the constraint
coupling matrix =
lincs-order              = 4
; Lincs will write a warning to the stderr if in one
step a bond =
;rotates over more degrees than =

 lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials =
morse                    = no

; NMR refinement stuff  =
; Distance restraints type: No, Simple or Ensemble =
disre                    = No
; Force weighting of pairs in one distance restraint:
Equal or Conservative =
disre-weighting          = Equal
; Use sqrt of the time averaged times the
instantaneous violation =
disre-mixed              = no
disre-fc                 = 1000
disre-tau                = 0
; Output frequency for pair distances to energy file =
nstdisreout              = 100

; Free energy control stuff =
free-energy              = no
init-lambda              = 0
delta-lambda             = 0

; Non-equilibrium MD stuff =
acc-grps                 =
accelerate               =
freezegrps               = Protein POPC SOL
freezedim                = Y Y Y Y Y Y Y Y Y
; Electric fields       =
; Format is number of terms (int) and for all terms an
amplitude (real) =
; and a phase angle (real) =
E-x                      =
E-xt                     =
E-y                      =
E-yt                     =
E-z                      =
E-zt                     =

; User defined thingies =
user1-grps               =
user2-grps               =
user3-grps               =
userint1                 = 0
userint2                 = 0
userint3                 = 0
userint4                 = 0
userreal1                = 0
userreal2                = 0
userreal3                = 0
userreal4                = 0


	
		
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