[gmx-users] system is bigger but box remains
taveechai taveecharoenkool
taweehui at yahoo.com
Fri Sep 9 11:02:21 CEST 2005
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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