[gmx-users] Re: REMD analysis

[Mark Abraham]

On Wed, May 22, 2013 at 2:19 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> Dear Sir,
>
> I performed another round of trial with different set of temperature and I
> got the avg accp. ration around 0.22. Here's the temp. dist. that I used :
> 250 268 288 308 331 355 380 408 438 469 503 540 579 621
>
> I then checked the replica_index and replica_temp files for each replica
> individually. The plots are exactly similar for all the replicas, as an eg.
> here's the link for first three replicas .
> https://www.dropbox.com/s/cuydj010wh2hgkt/replica_index0.png
> https://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.png
> https://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.png
> https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png
> https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png
> https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png
>
>
These are the same data. Whatever you are doing to generate them isn't what
you think you're doing :-)

Mark


> I checked the PE overlap also, that looks fine (
> https://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.png)
> I checked for the temp. dist. which also looks fine to me .
> https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png
>
> I don't know why all plots are similar ?? Is this related to wrong settings
> in mdp file. Here's the mdp file that I am using for production run. I
> changed ref_t for each replica in the mdp file.
>
>
> I suspect that I am doing something wrong somewhere ...
>
>  define              =  -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES
>  constraints         =  all-bonds
>  integrator          =  md
>  dt                  =  0.002  ; ps
>  nsteps              =  25000000; 50000 ps = 50 ns
>  nstcomm             =  10
>  nstcalcenergy       =  10
>  nstxout             =  1000     ; 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               =  250
>  ; Pressure coupling is off
>  Pcoupl              =  no
>  ; Generate velocites is on
>  gen_vel             =  yes
>  gen_temp            =  300
>  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  =  78.5    ; 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  = 0.005
>
>
> It will be helpful if you provide your comments...
>
> Regards
> --------------
> BHARAT
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