AMBER Archive (2004)

Subject: AMBER: simulated annealing

From: Abd Ghani Bin Abd Aziz (GS13161_at_mutiara.upm.edu.my)
Date: Wed Jul 28 2004 - 07:08:48 CDT

Dear amber,
 
i've problem with my simulated annealing MD. i try to heat my structure up to 400K but the output file showed that the maximum temperature is 300K and the output file showed that the structure is not recool to 10K. at the end of the simulation, the temperature still maintain at 300K and it completed the timestep that i set (15ps). why the temperature is not achieve to 400K? and why it's not recool to 10K at the of simulation.
 
Thank you
 
 
 
cd /home/ghaneiee/1jkmsim
cat << eof1 > simul_anneal.in
# 15ps simulated protocol
 &cntrl
  nstlim=15000, ntt=1,
  scee=1.2, igb=0, ntb=2, ntp=1, ntc=2,
  ntpr=50, pencut=0.1,
  ipnlty=1, vlimit=40,
 &end
#
# Simple simulated annealing algorithm:
#
# from steps 0 to 1000: raise target temperature 10-400K
# from steps 1000 to 3000: leave at 400K
# from steps 3000 to 15000: re-cool to low temperature
#
 &wt
  type='TEMP0', istep1=0, istep2=1000, value1=10.0, value2=400.0,
 &end
 &wt
  type='TEMP0', istep1=1001, istep2=3000, value1=400.0, value2=400.0,
 &end
 &wt
  type='TEMP0', istep1=3001, istep2=15000, value1=400.0, value2=10.0,
&end
#
# Strength if temperature coupling:
#
# steps 0 to 3000: tight coupling for heating and equilibration
# steps 3000 to 11000: slow cooling phase
# steps 11000 to 13000: somewhat faster cooling
# steps 13000 to 15000: fast cooling, like a minimization
#
 &wt
  type='TAUTP', istep1=0,istep2=1000, value1=0.1,value2=0.1,
&end
 &wt
  type='TAUTP', istep1=1001,istep2=2000,value1=0.1,value2=0.1,
&end
 &wt
  type='TAUTP', istep1=2001,istep2=13000,value1=5.0,value2=5.0,
&end
 &wt
  type='TAUTP', istep1=13001,istep2=14000,value1=4.0,value2=4.0,
&end
 &wt
  type='TAUTP', istep=14001,istep2=15000,value1=3.0,value2=3.0,
&end
#
# "Ramp up" the restraints over the first 3000 steps:
#
 &wt
  type='REST', istep1=0,istep2=2000,value1=0.1,value2=1.0,
 &end
 &wt
  type='REST', istep1=2001,istep2=15000,value1=1.0,value2=1.0,
 &end
 &wt  type='END' 
&end
LISTOUT=POUT
DISANG=RST.f
# Group definition
20.0
RES 101 270
RES 291 365
END
END
eof1
/usr/local/amber6/exe/sander -O -i simul_anneal.in -o simul_anneal.out -p 1jkm.prm -c 1jkm_min5.xyz -ref 1jkm_min5.xyz -r simul_anneal.xyz -x simul_anneal.crd
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