AMBER: simulated annealing

From: Lee SL <>
Date: Sat, 14 Aug 2004 05:51:14 -0400

hello amber users,

i have a question, is it okat to use ntt=3 (langevin dynamics) in simulated
annealing (SA) simulation, or i should stick to ntt=1? because in the manual
(im using amber8) it says in page 115, "TAUTP, used in temperature scaling
when temperature coupling options NTT=1 is used"

i tried running SA over and over again by adjusting here and there
(including switching ntt=3 to ntt=1, adjusting the tempi and temp0 etc). my
previous run which i used ntt=3, didnt really perform to what i expected,
the temperature stayed at 300K and the system was never heated up to 600K
(as what i want it to) so, i changed ntt=1, and it's still running tho. my
system contains 8654 atoms, here i append my SA script, i was hoping if any
of you could have a look at it and perhaps identify what i have been

i have read a few of the SA problems posted in this archive, and it did help
me a lot, and i also followed the simple script posted by Dr. Carlos
Simmerling using GB solvation, however, i still couldnt seem to get the
temperature to 600K. it maintains around 300+K

looking forward to get any feedbacks

thnak you in advance

my SA script:

simulated annealing for 20ps without restraints

nstlim=20000, imin=0, ntx=1, nmropt=1, ntb=0,
ntpr=100, ntwr=1000, ntwx=100,ntwe=100,
igb=2, saltcon=0.2, cut=15, scee=1.2,
ntt=1, dt=0.001,
ntc=2, ntf=2, vlimit=30,
#from steps 0 to 8000, heat from 10 to 600k
#from steps 8001 to 10000,maintain at 600K
#from steps 10001 to 20000, re-cool from 600 to 0K
TYPE='TEMP0', istep1=0, istep2=8000, value1=300.0, value2=600.0,
TYPE='TEMP0', istep1=8001, istep2=10000, value1=600.0, value2=600.0,
TYPE='TEMP0', istep1=10001, istep2=20000, value1=600.0, value2=0.0,
#strength for temperature coupling:
#steps 0 to 10000:tight coupling for heating and equilibration
#steps 10001 to 18000:slow cooling phase
#steps 18001 to 19000:faster cooling
#steps 19001 to 20000:fast cooling
TYPE='TAUTP', istep1=0, istep2=5000, value1=0.1, value2=0.1,
TYPE='TAUTP', istep1=5001, istep2=18000, value1=5.0, value2=5.0,
TYPE='TAUTP', istep1=18001, istep2=19000, value1=1.0, value2=1.0,
TYPE='TAUTP', istep1=19001, istep2=20000, value1=0.1, value2=0.05,

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Received on Mon Aug 16 2004 - 09:53:01 PDT
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