[gmx-users] Rerun same trajectory - Pulling

[Justin Lemkul]

On 12/25/12 8:41 AM, Steven Neumann wrote:
> Thank you Justin.
> It is weird I cannot reproduce it with the same mdp:
>
> 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 LIG_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
>
>
> Using:
>
> grompp -f pull3nmSnew.mdp -c npt298.gro -p topol.top -n index.ndx -t
> npt298.cpt -o pullS_2new.tpr
>
> As I take velocities from npt it should be reproducible but profiles
> force vs time looks similar with breaking point at different time.
>
> Can I edit somehow tpr file and change the frequency of frames only?
> Otherwise I have to run pulling again and US windows from scratch...
> quite time consuming.
>

The same .tpr file will not necessarily produce an identical result, so even if 
you could edit just the output interval, you would not necessarily achieve 
exactly the same thing.

http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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