[gmx-users] structure changed after energy minimization

Smith, Micholas D. smithmd at ornl.gov
Tue Sep 1 14:14:45 CEST 2015

Hi Sana Saeed,

What force field are you using? Also are you sure the structure you are starting with is stable to begin with? It is possible that the model you are starting with is actually fairly far away from the minimum energy structure in which case energy minimization may alter the structure (though i've never seen a beta sheet changing into a coil-like form). 


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sana Saeed <bioinformatic.lady at yahoo.com>
Sent: Monday, August 31, 2015 10:30 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] structure changed after energy minimization

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

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