[gmx-users] remd

[Richard Broadbent]

Not sure exactly what merging together means, for visualisation I 
generally use vmd as this supports gromacs files directly.

Your problem might be to do with, using rlist, rcoulomb, and rvdw set to 
0 is not the standard way to do an infinite cut-off normally you set 
them to -1 as in the manual.

Also the AMBER force field was parametrised with a cut-off it might, 
depending on what you are trying to do, be advisable to use the cut-off 
specified in the original papers and the wider literature for the AMBER 
force field.

Richard

On 02/07/13 10:07, Shine A wrote:
> 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
>