On 8/16/12 12:57 PM, tarak karmakar wrote:
Dear All,
In my simulation I want the temperature of the system to be reached at
300 K only after 3 ps. But after 3ps I see temperature became 402 K.
So am I doing any mistake in the '.mdp' file given below?
You have a few.
1. You should not run MD with flexible water.
2. Finite cutoffs lead to rounding errors and accumulation of heat. This is
most likely the source of your problem. I seem to recall Mark (or maybe someone
else) already told you about this point.
-Justin
define = -DFLEXIBLE
constraints = h-bonds
integrator = sd
dt = 0.001 ; 1fs
nsteps = 3000 ; 3ps
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
pbc = no
table-extension = 20.0
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 3
annealing_temp = 0 300
ld_seed = 8072012
;temperature coupling is on
Tcoupl = berendsen
tau_t = 0.01
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
Thanks,
--
========================================
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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