On 13/08/2012 4:09 AM, tarak karmakar wrote:
Dear All,
I did the simmulated annealing for a protein where I wanted to
increase the temperature from 0 K to 300 K after 300 ps. But after the
simulation run I see the temp got increased up to 400 K and so.
So can anyone tell me whether I am doing any mistake ?
Don't know, you gave us the .mdp file for the run you thought worked,
and not the one for the run you think might have a problem.
The .mdp file for the run is as follows. The temperature plot has been
attached with this mail.
Attachments are not accepted. You will need to upload to an online
file-sharing provider and give a URL if you want to share such.
define = -DFLEXIBLE
constraints = h-bonds
integrator = sd
dt = 0.001 ; 1fs
nsteps = 300000 ; 300 ps
nstcomm = 1
nstxout = 1000 ; frequency to write
coordinates to output trajectory
nstvout = 0 ; frequency to write
velocities to output trajectory; the last velocities are always
written
nstfout = 0 ; frequency to write forces to
output trajectory
nstlog = 10 ; frequency to write energies
to log file
nstenergy = 100 ; frequency to write energies to edr file
nstcalcenergy = 100
vdwtype = cut-off
coulombtype = cut-off
Excess heating from the artefacts of this method might be expected.
pbc = no
table-extension = 20.0
This is much larger than you should need, but is not a problem. Do not
attempt to work around
http://www.gromacs.org/Documentation/Terminology/Blowing_Up with this
setting.
Mark
nstlist = 100
ns_type = grid
rlist = 1.0
rcoulomb = 1.2
rvdw = 1.2
comm-mode = angular
comm-grps = system
optimize_fft = yes
;heating
annealing = single
annealing_npoints = 2
annealing_time = 0 300
annealing_temp = 0 300
ld_seed = 8072012
; V-rescale temperature coupling is on
Tcoupl = no
tau_t = 0.02
tc_grps = system
ref_t = 0
; Pressure coupling is off
Pcoupl = no
; Generate velocites is on
gen_vel = yes
gen_temp = 0
gen_seed = 8042012
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