Dear All,
I am trying to minimize a protein using Simulated Annealing method
implemented in Gromacs3.3. I am giving the annealing points a 4 for temp
400,350,300,250 for 10ps, but i am not getting the temperature change in
the log. Its just coming as 0 temperature only. I am using Langevin
dynamics for temperature control. Here is my mdp file:
title = TGR model minimization thru SA
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 50000
dt = 0.02
init_step = 0
;langevin dynamics
bd_fric = 1
ld_seed = 1993
;minimization
emtol = 100
emstep = 1.0
;output control
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 100
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000
xtc_grps =
energygrps =
; Neighbor searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.5
; electrostatics
coulombtype = PME
rcoulomb = 1.5
epsilon_r = 1.0
; van der waals params
vdwtype = cutoff
rvdw = 2.0
; table params
table-extension = 3
;PME params for ewald calc.
fourierspacing = 0.15
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; temperature coupling
tcoupl = no
; pressure coupling
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.2
compressibility = 4.5e-5
ref_p = 1.01325
; simulated annealing params
annealing = single
annealing_npoints = 4
annealing_time = 0 10 10 10
annealing_temp = 400 350 300 250
;velocity generation
gen_vel = no
gen_temp = 400
gen_seed = 1732529
If somebody can figure out what i am missing out, it will really be a
great help..
thanks in advance,
regards,
Monika
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