bipin singh wrote:
Hello users,
I have some doubt regarding the reference temperature(ref_temp)option
during simulated annealing, i mean in the .mdp for simulated annealing
what should be the correct ref_temp i.e. 0 K(starting temerature) or the
target temperature(328K) and accordingly what should be the value for
gen_temp(0K or 328K).
AFAIK, ref_t is ignored during annealing, since the heating is controlled by a
separate algorithm. The gen_temp issue is more complex - how does one even
represent 0 K, as the velocities are zero? I don't know what grompp might do if
you set "gen_temp = 0" in the .mdp file. Try it and see. The success or
failure of annealing will be very obvious, even with a short simulation.
-Justin
The part of my mdp file for the simulated annealing is as follows:
;Annealing
annealing=single
annealing_temp=0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300
320 328
annealing_npoints=18
annealing_time=0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300
320 340
;Temperature coupling is on in two groups
Tcoupl= V-rescale
tau_t= 0.1
tc-grps= System
ref_t= 328
pbc= xyz ; 3-D PBC
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
compressibility= 4.5e-5
; Generate velocites is on at 328 K.
gen_vel= yes ; assign velocities from Maxwell distribution
gen_temp= 328.0 ; temperature for Maxwell distribution
gen_seed= 173529;generate a random seed
--
/
---------------------------------
Thanks and regards
/Bipin Singh/
/
/
/
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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