[gmx-users] system is bigger but box remains
Alan Dodd
anoddlad at yahoo.com
Fri Sep 9 12:31:30 CEST 2005
I've occasionally had a similar problem myself. So
far it's always been one of two things. Either I've
used -shuffle -sort for a multiple node run, and not
deshuffled it afterwards/deshuffled it wrong, or the
initial confersion to a .gro file has been wrong in
some way. If noone comes up with something more
helpful it may be worth producing your .gro file in a
marginally different way, I've evolved a highly
convoluted system to stop my bilayers going "weird"
when I initially convert them from pdbs. Or just make
sure your topology etc. is absolutely correct,
especially the lipid part.
--- taveechai taveecharoenkool <taweehui at yahoo.com>
wrote:
> 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 =
>
=== message truncated ===
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