thank you for responding,
attached are the output files for both SA run done using ntt=3
(anneal2.gb.out) and ntt=1 (anneal3.gb.out).
for ntt=3, i didnt wait till the run finish, coz i didnt want to waste
computer resources, i killed the job halfway coz the temperature didnt seem
to increase.
for the run with ntt=1, the job is still running, and attached is the latest
output file, however, the temperature didnt reach 600K as expected, the
highest temperature is only 400++ K,
i hope you can help me figure out whats wrong with my input files
by the way, is it okay to use ntt=3 in simulated annealing?
thank you
----- Original Message -----
From: "Carlos Simmerling" <carlos.ilion.bio.sunysb.edu>
To: <amber.scripps.edu>
Sent: Saturday, August 14, 2004 8:20 PM
Subject: Re: AMBER: simulated annealing
> 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.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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Received on Mon Aug 16 2004 - 09:53:01 PDT
