[gmx-users] structure changed after energy minimization

[Sana Saeed]

hi gmx users,i want to simulate prion protein(beta-sheets structure; model in modeller), but after minimization the structure totally changes into elongated form.what am i missing? i am doing implicit solvent simulation. this is the mdp file for minimization:  title               =cpp                 =  /lib/cpp                                                 ; prepocessor of the current machinedefine              =  -DFLEXIBLE                                               ; -DPOSRES, -DPOSRES_IONS ;DFLEX_SPC; FLEXible SPC and POSition REStraints
integrator          =  steep                                                    ; steepest descent algorithmdt                  =  0.005                                                    ; time step in psnsteps              =  5000                                                     ; number of steps
emtol               =  100                                                      ; convergence criterionemstep              =  0.05                                                     ; intial step sizeconstraints           = noneconstraint-algorithm  = lincsunconstrained-start   = no                                                      ; Do not constrain the start configuration;shake_tol           = 0.0001nstlist             =  1                                                        ; step frequency for updating neighbour listns_type             =  simple                                                   ; grid ; method for nighbour searching (?)nstxout             =  100                                                      ; frequency for writing coords to outputnstvout             =  100                                                      ; frequency for writing velocities to outputnstfout             =  0    ; frequency for writing forces to outputnstlog              =  100    ; frequency for writing energies to log filenstenergy           =  100  ; frequency for writing energies to energy filenstxtcout           =  0    ; frequency for writing coords to xtc trajxtc_grps            =  system ; group(s) whose coords are to be written in xtc trajenergygrps          =  system ; group(s) whose energy is to be written in energy filepbc                 =  xyz    ; use pbcrlist               =  1.0    ; cutoff (nm)coulombtype         =  cutoff ; truncation for minimisation, with large cutoffrcoulomb            =  1.0vdwtype             =  cut-off  ; truncation for minimisation, with large cutoffrvdw                =  1.0nstcomm             =  0  ; number of steps for centre of mass motion removal (in vacuo only!)Tcoupl              =  noPcoupl              =  nogen_vel             =  no Free energy control stufffree_energy              = yesinit_lambda              = 0.0delta_lambda             = 0sc_alpha                 =0.5sc-power                 =1.0sc-sigma                 = 0.3