Hi G,
I use the following simulated annealing protocol for nucleic acids in
AMBER9. I'm pretty sure I got this from a tutorial. This may not
work for the system you have in question, but it should give you a
start.
"Simulated Annealing Protocol, 50 ps - Case=199
&cntrl
imin=0,
ntpr=200,ntwr=10000,ntwx=200,
ntb=0,cut=20,vlimit=10,
ntt=1,nstlim=50000,dt=0.001,
ig=398,
igb=1,saltcon=1.0,offset=0.13,
pencut=-0.001, nmropt=1,
/
&ewald
eedmeth=5,
/
#
#Simulated annealing algorithm:
#
#from steps 0 to 5000: heat the system to 3000K
#from steps 5001 to 10000: cool the system to 2000K
#from steps 10001 to 15000: cool the system to 1000K
#from steps 15001 to 20000: cool the system to 800K
#from steps 20001 to 25000: cool the system to 600K
#from steps 25001 to 30000: cool the system to 400K
#from steps 30001 to 35000: cool the system to 200K
#from steps 35001 to 40000: cool the system to 100K
#from steps 40001 to 50000: cool the system to 0K
#
&wt type='TEMP0', istep1=0,istep2=5000,value1=3000.0,
value2=3000.0, /
&wt type='TEMP0', istep1=5001,istep2=10000,value1=3000.0,
value2=2000.0, /
&wt type='TEMP0', istep1=10001,istep2=15000,value1=2000.0,
value2=1000.0, /
&wt type='TEMP0', istep1=15001,istep2=20000,value1=1000.0,
value2=800.0, /
&wt type='TEMP0', istep1=20001, istep2=25000, value1=800.0,
value2=600.0, /
&wt type='TEMP0', istep1=25001, istep2=30000, value1=600.0,
value2=400.0, /
&wt type='TEMP0', istep1=30001, istep2=35000, value1=400.0,
value2=200.0, /
&wt type='TEMP0', istep1=35001, istep2=40000, value1=200.0,
value2=100.0, /
&wt type='TEMP0', istep1=40001, istep2=50000, value1=100.0,
value2=0.0, /
&wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
value2=0.4, /
&wt type='TAUTP', istep1=5001,istep2=15000,value1=4.0,
value2=4.0, /
&wt type='TAUTP', istep1=15001,istep2=30000,value1=1.0,
value2=1.0, /
&wt type='TAUTP', istep1=30001,istep2=50000,value1=0.1,
value2=0.05, /
&wt type='REST', istep1=0,istep2=5000,value1=0.1,
value2=1.0, /
&wt type='REST', istep1=5001,istep2=50000,value1=1.0,
value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DISANG=RST
EOF"
-Dave
On 5/9/11, Guenegou, Guillaume [ORDFR] <GGUENEGO.its.jnj.com> wrote:
> Dear all,
>
> I am trying to implement a simulated annealing protocol with amber 11.
>
> The goal is to cool more or less slowly a snapshot with sander method.
> For exemple, the snapshot is at 300K and with several sander
> calculations, I cool it until 0K.
>
>
>
> I would like to know if someone has already done a similar process and
> as a consequence, can give me advices regarding some parameters values
> (ie nstlim, dt, ...).
>
>
>
> Is there any recommended number of sander steps to make this temperature
> decrease?
>
>
>
> Thanks in advance
>
> Regards
>
> G.GUENEGOU
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon May 09 2011 - 08:00:05 PDT
