[gmx-users] Minimization Issue - membrane inverted and system copied
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Sep 21 21:31:57 CEST 2006
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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--
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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