[gmx-users] Rerun same trajectory - Pulling
s.neumann08 at gmail.com
Tue Dec 25 14:41:27 CET 2012
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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