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
--
========================================
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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