[gmx-users] Rerun same trajectory - Pulling

[Steven Neumann]

Maybe I wrote it wrote it wrong.

I have 1500 frames of which with 0.1 nm spacing I have chosen 14 to
run umbrella sampling windows.

I used:

conf0.gro
conf140.gro
conf213.gro
conf262.gro
conf263.gro
conf300.gro
...
conf1500.gro

However, the moment when my ligand became dettached is very short
(beween conf conf262.gro and 263.gro) that there is a gap in
histograms. So I need the same pulling trajectory but with more frames
e.g. 10 times higher.

when I use grommp -f new.mdp -o new.tpr
mdrun -rerun oldPull.xtc -s new.tpr -deffnm new

I dont get my new.xtc ... Hoiw can I solve it?

Steven

On Tue, Dec 25, 2012 at 8:27 AM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> 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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