[gmx-users] Rerun same trajectory - Pulling
s.neumann08 at gmail.com
Tue Dec 25 14:53:41 CET 2012
The other option would be to decrease force constant in two windows in
between of which is the gap. Then histograms for them willl be more
wide and they will overlap. Is that possible to combine windows using
WHAM with different force constants?
On Tue, Dec 25, 2012 at 1:41 PM, Steven Neumann <s.neumann08 at gmail.com> 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
> 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.
> On Tue, Dec 25, 2012 at 1:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 12/25/12 3:51 AM, Steven Neumann wrote:
>>> 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:
>>> 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?
>> Because, as I said, that's not what the -rerun function does. The -rerun
>> function simple re-evaluates the energies of the existing frames according
>> to the topology in the .tpr file, thus allowing you to re-calculate energy
>> terms based on new energy groups or a modified topology. If a frame does
>> not exist, you cannot create it magically. If you didn't save the frame you
>> needed, you need to run a new simulation. There is no way to interpolate
>> new frames.
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list gmx-users at gromacs.org
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