[gmx-users] Rerun same trajectory - Pulling

[Justin Lemkul]

On 12/24/12 5:53 PM, Steven Neumann wrote:
> 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.
>

You can't create frames that aren't there, unfortunately.  Saving every 0.2 ps 
is usually vast overkill; if you have a gap in the sampling, you probably need 
more windows rather than more frames in the existing ones.

-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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