On 12/25/12 8:41 AM, Steven Neumann 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
Using:
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.
The same .tpr file will not necessarily produce an identical result, so even if
you could edit just the output interval, you would not necessarily achieve
exactly the same thing.
http://www.gromacs.org/Documentation/Terminology/Reproducibility
-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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