[gmx-users] Rerun same trajectory - Pulling

[Steven Neumann]

Dear Gmx Users,

I run pulling simulation of my ligand away from the protein. I
produced 1500 frames and run US windows with 0.1 nm spacing. However,
I have a gap in histograms - I need to use lower value of nstxtcout to
get the proper window where the gap is as the time it goes away is
really short.

 How can I rerun the same trajectory with lower nstxtcout ? I do not
want to use grompp as from the same mdp file with pulling simulation I
get different trajectories. My mdp (it is continuation after nvt and
npt respectively):

title       = Umbrella pulling simulation
define      = -DPOSRES_T
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 150000    ; 0.3 ns
nstcomm     = 10
; Output parameters
nstxout     = 0
nstvout     = 0
nstxtcout   = 100       ; every 1 ps 1500 frames
nstenergy   = 500
; 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        = 1.2
vdwtype     = Switch
rvdw-switch = 1.0
; 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
; Temperature coupling is on
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc_grps     = Protein FE_Water_and_ions   ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 298   298                     ; reference temperature,
one for each group, in K
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 2.0
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     = GLU
pull_group1     = LIG
pull_rate1      = 0.01      ; 0.001 nm per ps = 1 nm per ns
pull_k1         = 2000      ; kJ mol^-1 nm^-2

Shall I use rerun option of mdrun? But I wont be able to change
frequency of frames.

Please help,

Merry Christmas :)

Steven