[gmx-users] remd

[Shine A]

Sir,

      I did a 10 ns  REMD simulation for a peptide, 8 replicas using amber
force field.Then extracted pdb file from the trajectory and clustered using
g_cluster. The I viewed the average structure of the cluster in pymol .But
here the atoms are merged togather.why it happends?Is there any problem
with my force field? My md.mdp file as follows.

RESHELIX ; -DFLEXIBLE -DPOSRES
 constraints         =  none
 integrator          =  md
 dt                  =  0.001   ; ps
 nsteps              =  10000000 ; 10000 ps = 10 ns
 nstcomm             =  10
 nstcalcenergy       =  10
 nstxout             =  500     ; frequency to write coordinates to output
 trajectory
 nstvout             =  0       ; frequency to write velocities to output
 trajectory; the last velocities are always written
 nstfout             =  0       ; frequency to write forces to output
 trajectory
 nstlog              =  1000         ; frequency to write energies to log
 file
 nstenergy           =  1000     ; frequency to write energies to edr file

 vdwtype             =  cut-off
 coulombtype         =  cut-off

 pbc                 =  no

 nstlist             =  0
 ns_type             =  simple
 rlist               =  0       ; this means all-vs-all (no cut-off), which
 gets expensive for bigger systems
 rcoulomb            =  0
 rvdw                =  0

 comm-mode           =  angular
 comm-grps           =  system

 optimize_fft        =  yes

 ; V-rescale temperature coupling is on
 Tcoupl              =  v-rescale
 tau_t               =  0.1
 tc_grps             =  system
 ref_t               =  376.32
 ; Pressure coupling is off
 Pcoupl              =  no
 ; Generate velocites is on
 gen_vel             =  yes
 gen_temp            =  270
 gen_seed            =  -1

 ;
 ; Implicit solvent
 ;
 implicit_solvent    =  GBSA
 gb_algorithm        =  Still ; HCT ; OBC
 nstgbradii          =  1
 rgbradii            =  0   ; [nm] Cut-off for the calculation of the
Born radii. Currently must be equal to rlist
 gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit
solvent
 ; gb_saltconc       =  0     ; Salt concentration for implicit
solvent   models, currently not used
 sa_algorithm        =  Ace-approximation
 sa_surface_tension  = -1