[gmx-users] Rerun same trajectory - Pulling

[Steven Neumann]

On Tue, Dec 25, 2012 at 2:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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

O course I know! This is why I want to rerun my pulling simulation to
get more frames for umbrella sampling windows and no to waste windows
I have already run - hence I need exactly the same trajectory.

grompp -f new.mdp ... -o new.tpr
mdrun -s new.tpr -rerun oldPull.xtc -deffnm new

Is that correct?
>
> --
> ========================================
>
> 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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