AMBER Archive (2004)

Subject: RE: AMBER: simulated annealing

From: Lee SL (leesl66_at_hotmail.com)
Date: Sat Aug 14 2004 - 05:40:54 CDT

oopss.. i seemed to have appended the wrong annealing.in file, here is the
correct one. sorry everybody

simulated annealing for 20ps without restraints

&cntrl
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,
tempi=10.0,
ntt=1, dt=0.001,
ntc=2, ntf=2, vlimit=30,
/
&ewald
eedmeth=5,
/
#simple simulated annealing script
#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
&wt
TYPE='TEMP0', istep1=0, istep2=8000, value1=10.0, value2=600.0,
/
&wt
TYPE='TEMP0', istep1=8001, istep2=10000, value1=600.0, value2=600.0,
/
&wt
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:somewhat faster cooling
#steps 19001 to 20000:fast cooling,like a minimization
&wt
TYPE='TAUTP', istep1=0, istep2=10000, value1=0.1, value2=0.1,
/
&wt
TYPE='TAUTP', istep1=10001, istep2=18000, value1=5.0, value2=5.0,
/
&wt
TYPE='TAUTP', istep1=18001, istep2=19000, value1=1.0, value2=1.0,
/
&wt
TYPE='TAUTP', istep1=19001, istep2=20000, value1=0.1, value2=0.05,
/
&wt
TYPE='END',
/
&rst
iat(1)=0,
/

>From: "Lee SL" <leesl66_at_hotmail.com>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: AMBER: simulated annealing
>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
>missing.
>
>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
>
>&cntrl
>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,
>tempi=10.0,
>ntt=1, dt=0.001,
>ntc=2, ntf=2, vlimit=30,
>/
>&ewald
>eedmeth=5,
>/
>#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
>&wt
>TYPE='TEMP0', istep1=0, istep2=8000, value1=300.0, value2=600.0,
>/
>&wt
>TYPE='TEMP0', istep1=8001, istep2=10000, value1=600.0, value2=600.0,
>/
>&wt
>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
>&wt
>TYPE='TAUTP', istep1=0, istep2=5000, value1=0.1, value2=0.1,
>/
>&wt
>TYPE='TAUTP', istep1=5001, istep2=18000, value1=5.0, value2=5.0,
>/
>&wt
>TYPE='TAUTP', istep1=18001, istep2=19000, value1=1.0, value2=1.0,
>/
>&wt
>TYPE='TAUTP', istep1=19001, istep2=20000, value1=0.1, value2=0.05,
>/
>&wt
>TYPE='END',
>/
>&rst
>iat(1)=0,
>/
>
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