[gmx-users] About plumed gromacs umbrella pulling

[vidhya sankar]

Dear jusitn Thank you for your previous reply.
                                                                          I am doing Umbrella sampling using plumed-gromacs. for that i have done umbrella pulling using gromacs only 

I have extracted the frame of reference from 120ps to 360ps . i am using these set of trajectories for the Umbrella sampling in plumed gromacs (interface with plumed)
when i do the sampling using plumed-gromacs i used gromacs  mdp files with option of  tinit =120  while i define all these extracted pdbs (from 120 to 360ns) in plumed .dat file . is it  appropriate  ?  i Think when plumed-gromacs    do the sampling, it consider from 120 to 360 ns trajectories only. is it correct?. i have provided the plumed.dat and md.mdp file as below kindly consider and go through it  . i am expecting your valuable  reply
       PRINT W_STRIDE 100 
        S_PATH TYPE RMSD FRAMESET mdoutput  NFRAMES 24 LAMBDA 72.634290 
        Z_PATH TYPE RMSD FRAMESET mdoutput  NFRAMES 24 LAMBDA 72.634290 
        UMBRELLA CV 1 KAPPA 1000 AT     0.000000
        UMBRELLA CV 2 KAPPA 1000 AT     0.000000
        ENDMETA


title       = Umbrella pulling simulation 
define      = -DPOSRES_B
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 120
nsteps      = 250000    ;
nstcomm     = 10
; Output parameters
nstxout     = 50      ; 
nstvout     = 50 
nstfout     = 50
nstxtcout   = 50      
nstenergy   = 50
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes       ; continuing from NPT 
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid 
rlist       = 1.4
rcoulomb    = 1.4
rvdw        = 1.4
; PME electrostatics parameters
coulombtype    =  PME  
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl      = Nose-Hoover
tc_grps     = Protein   Non-Protein 
tau_t       = 0.5       0.5
ref_t       = 310       310
; SIMULATED ANNEALING  
; Type of annealing for each temperature group (no/single/periodic)
;annealing                = periodic single
; Number of time points to use for specifying annealing in each group
;annealing_npoints        = 5 3
; List of times at the annealing points for each group
;annealing_time           = 0 3 6 9 12  0 2 4
; Temp. at each annealing point, for each group.
;annealing_temp          = 310 320 298 298 310  310 320 310
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman 
pcoupltype      = isotropic
tau_p           = 1.0       
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocities is off
gen_vel     = no 
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
;pull            = umbrella
;pull_geometry   = distance  ; simple distance increase 
;pull_dim        = N N Y
;pull_start      = yes       ; define initial COM distance > 0
;pull_ngroups    = 1
;pull_group0     = Chain_B 
;pull_group1     = Chain_A 
;pull_rate1      = 0      ; 0.01 nm per ps = 10 nm per ns
;pull_k1         = 1000      ; kJ mol^-1 nm^-2
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