AMBER Archive (2004)

Subject: Re: AMBER: simulated annealing

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sat Aug 14 2004 - 07:20:12 CDT

did you look carefully at the sander output to see if it read the weight
changes properly? send the output all the way up until step 1 energies and
I will look at it.

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Lee SL wrote:

>
> 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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