[gmx-users] Re: REMD analysis

[bharat gupta]

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/cuydj010wh2hgkt/replica_index0.png;cid=1368714426780-10>
https://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.png<https://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.png;cid=1368714426780-10>
https://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.png<https://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.png;cid=1368714426780-10>
https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png<https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png;cid=1368714426780-10>
https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png<https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png;cid=1368714426780-10>
https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png<https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png;cid=1368714426780-10>

I checked the PE overlap also, that looks fine (
https://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.png<https://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.png;cid=1368714426780-10>
)
I checked for the temp. dist. which also looks fine to me .
https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png<https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png;cid=1368714426780-10>

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.




 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

I suspect that I am doing something wrong somewhere ...

It will be helpful if anybody can help me in this regard...

Regards
--------------
BHARAT