[gmx-users] Minimization Issue - membrane inverted and system copied

[Arneh Babakhani]

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