[gmx-users] Minimization Issue - membrane inverted and system copied
Arneh Babakhani
ababakha at mccammon.ucsd.edu
Thu Sep 21 21:58:04 CEST 2006
Ahh! Yes, Indeed I did center it to 0 0 0. I corrected that (centered
it in the box), and it works fine now.
Thanks Tsjerk,
Regards,
Arneh
Tsjerk Wassenaar wrote:
> Hi Arneh,
>
> I guess it's the PBC. Did you center your bilayer at z=0 (or x, or y)?
> Then it's certain it's the PBC. Next time it may be better to center
> your system at the box center.
>
> Best,
>
> Tsjerk
>
> On 9/21/06, Arneh Babakhani <ababakha at mccammon.ucsd.edu> wrote:
>> Hi,
>>
>>
>> I'm getting a quirky result from my minimization of my system (which
>> consists of a small peptide in a membrane, solvated).
>>
>>
>> When I look at the trr of the minimization (or the outputted structure
>> after minization), I notice that my membrane has been inverted, and
>> there are 4 copies of the system. (Yes, i have my images setting in VMD
>> set for just the self structure).
>>
>>
>> What's going on here? My structure, topology and mdp files are all
>> correct (I successfully executed previous minimizations with them). I'm
>> sure it's something really obvious, by I can't figure it out. Would
>> appreciate any help.
>>
>>
>> Regards,
>>
>>
>> Arneh
>>
>>
>>
>> ; VARIOUS PREPROCESSING OPTIONS =
>> title =
>> cpp = /usr/bin/cpp
>> include =
>> define = -DFLEX_SPC
>>
>> ; RUN CONTROL PARAMETERS =
>> integrator = steep
>> ; start time and timestep in ps =
>> tinit = 0
>> dt = 0.002
>> nsteps = 5000
>> ; mode for center of mass motion removal =
>> comm-mode = Linear
>> ; number of steps for center of mass motion removal =
>> nstcomm = 1
>> ; group(s) for center of mass motion removal =
>> comm-grps =
>>
>> ; 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 = 10
>> emstep = 0.01
>> ; Max number of iterations in relax_shells =
>> niter = 20
>> ; Step size (1/ps^2) for minimization of flexible constraints =
>> fcstep = 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 = 100
>> nstvout = 100
>> nstfout = 0
>> ; Output frequency for energies to log file and energy file =
>> nstlog = 100
>> nstenergy = 100
>> ; Output frequency and precision for xtc file =
>> nstxtcout = 0
>> 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 =
>>
>> ; NEIGHBORSEARCHING PARAMETERS =
>> ; nblist update frequency =
>> nstlist = 10
>> ; ns algorithm (simple or grid) =
>> ns_type = grid
>> ; Periodic boundary conditions: xyz or no =
>> pbc = xyz
>> ; nblist cut-off =
>> rlist = 1
>> 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
>> ; Apply long range dispersion corrections for Energy and Pressure =
>> DispCorr = No
>> ; Spacing for the PME/PPPM FFT grid =
>> fourierspacing = 0.12
>> ; 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-5
>> ewald_geometry = 3d
>> epsilon_surface = 0
>> optimize_fft = yes
>>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
>> ; Temperature coupling =
>> Tcoupl = no
>> ; Groups to couple separately =
>> tc-grps =
>> ; Time constant (ps) and reference temperature (K) =
>> tau-t =
>> ref-t =
>> ; Pressure coupling =
>> Pcoupl = no
>> Pcoupltype = Isotropic
>> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
>> tau-p = 1
>> compressibility =
>> ref-p =
>>
>> ; SIMULATED ANNEALING CONTROL =
>> annealing = no
>> ; Time at which temperature should be zero (ps) =
>> zero-temp_time = 0
>>
>> ; GENERATE VELOCITIES FOR STARTUP RUN =
>> gen_vel = no
>> gen-temp = 300
>> gen-seed = 173529
>>
>> ; OPTIONS FOR BONDS =
>> constraints = none
>> ; Type of constraint algorithm =
>> constraint-algorithm = Lincs
>> ; Do not constrain the start configuration =
>> unconstrained-start = no
>> ; Use successive overrelaxation to reduce the number of shake
>> iterations =
>> Shake-SOR = no
>> ; Relative tolerance of shake =
>> shake-tol = 1e-04
>> ; 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
>>
>> ; ENERGY GROUP EXCLUSIONS =
>> ; Pairs of energy groups for which all non-bonded interactions are
>> excluded =
>> energygrp_excl =
>>
>> ; NMR refinement stuff =
>> ; Distance restraints type: No, Simple or Ensemble =
>> disre = No
>> ; Force weighting of pairs in one distance restraint: Conservative or
>> Equal =
>> disre-weighting = Conservative
>> ; 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
>> ; Orientation restraints: No or Yes =
>> orire = no
>> ; Orientation restraints force constant and tau for time averaging =
>> orire-fc = 0
>> orire-tau = 0
>> orire-fitgrp =
>> ; Output frequency for trace(SD) to energy file =
>> nstorireout = 100
>>
>> ; Free energy control stuff =
>> free-energy = no
>> init-lambda = 0
>> delta-lambda = 0
>> sc-alpha = 0
>> sc-sigma = 0.3
>>
>> ; Non-equilibrium MD stuff =
>> acc-grps =
>> accelerate =
>> freezegrps =
>> freezedim =
>> cos-acceleration = 0
>>
>> ; 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 =
>> userint1 = 0
>> userint2 = 0
>> userint3 = 0
>> userint4 = 0
>> userreal1 = 0
>> userreal2 = 0
>> userreal3 = 0
>> userreal4 = 0
>>
>>
>>
>>
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