[gmx-users] ref_temp and gen_temp during simulated annealing

[Justin A. Lemkul]

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/
> /
> /
> /
> 

-- 
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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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