AMBER Archive (2009)

Subject: Re: [AMBER] Simulated annealing

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Feb 26 2009 - 10:27:04 CST

not sure what you mean by changing strength of coupling, I'm not sure why
that would be needed during annealing. don't you just want to change temp0?
MD stability may depend a lot on how high a temperature you use. also, if
you go above 400K or so, make sure to use chirality and amide restraints to
avoid flips.

On Thu, Feb 26, 2009 at 11:22 AM, Hu, Shaowen (JSC-SK)[Universities Space
Research Association (USRA)] <shaowen.hu-1_at_nasa.gov> wrote:

> Dear Dr. Simmerling,
>
> Could you please share your SA input file with ntt=3. I tried before but I
> do not know how to change the strength of temperature coupling.
>
> Thanks a lot,
> Shaowen
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Carlos Simmerling
> Sent: Thursday, February 26, 2009 9:56 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Simulated annealing
>
> if you use ntt=1 and ntx>1 then ig really has no effect. with nx>3 you are
> telling sander to use your own velocities, so the random numbers do not get
> used in the calculation unless you set ntt=3. I have done annealing with
> ntt=3 with no trouble, I'm not ure why you would have bad results. another
> option you might try is to slightly change the temp0 variable. or do a
> single MD run and extract multiple coordinates to use as input coordinates
> for the multiple MD runs.
>
> On Thu, Feb 26, 2009 at 10:28 AM, Ibrahim Moustafa <I.moustafa_at_psu.edu
> >wrote:
>
> > Hi,
> >
> > I thought TEMPI has no effect if NTX>3 (in my case NTX=5) according to
> the
> > manual. I tried "ntt=3" but the system was very ill-behaving with
> gamma_ln
> > <
> > 5; I had to use "gamma_ln=100" which is far from the recommended values.
> > Also, I checked the archive for SA and I came across a previous post
> > mentioned "ntt=1" is more suitable for SA than "ntt=3"; LN is not good
> for
> > fast heating needed for SA. "ntt=1" seems working fine apart from the
> > repetitive behavior mentioned in my previous post. I'll try to set
> "tempi"
> > and see. If it did not work, I'll try perturbing the coordinates for each
> > cycle.
> >
> > thanks for the reply,
> > Ibrahim
> >
> > On 2/25/09 8:31 PM, "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
> > wrote:
> >
> > > check tempi- unless it is greater then 0 ig won't set velocities. also
> > > you might want ntt equal 3 using langevin dynamics, then ig will
> > > change the thermostat.
> > >
> > > On 2/25/09, Ibrahim Moustafa <I.moustafa_at_psu.edu> wrote:
> > >> Dear all,
> > >>
> > >> Iım trying to run a Simulated Annealing for a protein in which two
> > loops
> > >> missing from the crystal structure are modeled.
> > >> Those regions from the structure are restrained. I use the GB model
> for
> > the
> > >> simulation using the input file given below.
> > >> The plan was to apply the SA for 10 cycles, each starting with a new
> set
> > of
> > >> velocities by changing ³ig values² every time randomly. The simulation
> > runs
> > >> fine; BUT the output is exactly the same for all simulations. I
> expected
> > to
> > >> see different trajectories in the different simulations. This
> repetitive
> > >> behavior
> > >> is odd suggesting that something is not right going on. Two examples
> > for
> > >> the output from two runs are shown below.
> > >> Iıd appreciate if someone can point me to why I see this behavior
> during
> > SA?
> > >> And what is faulty in the protocol used?
> > >> This simulation starts using a restart file from 50 ps MD to bring the
> > >> system from 0-300 K. Originally, I used ³irest=1² as in the tutorial
> of
> > Dr.
> > >> Ross
> > >> and saw the same behavior. Then, I tried ³irest=0² but it did not
> solve
> > the
> > >> problem.
> > >>
> > >>
> > >>> INPUT FILE
> > >>
> > >> &cntrl
> > >> imin=0, irest=0, ntx=5,
> > >> nstlim=200000, dt=0.0005,
> > >> ntpr=500, ntwx=10000, ntwr=1000,
> > >> ntt=1,
> > >> ntc=2, ntf=2,
> > >> ntb=0, nsnb=10, scee=1.2,
> > >> ntr=1, restraint_wt=10, restraintmask=':1-134 | :145-183 |
> :200-628',
> > >> cut=25, rgbmax=25, ntb=0, igb=5, vlimit=10, ig=600129,
> > >> nmropt=1,
> > >> &end
> > >> &ewald
> > >> eedmeth=5,
> > >> &end
> > >> &wt
> > >> type='TEMP0', istep1=0, istep2=20000,
> > >> value1=300, value2=800,
> > >> &end
> > >> &wt
> > >> type='TEMP0', istep1=20001, istep2=60000,
> > >> value1=800, value2=800,
> > >> &end
> > >> &wt
> > >> type='TEMP0', istep1=60001, istep2=200000,
> > >> value1=800, value2=300,
> > >> &end
> > >> # Strength of Temp coupling
> > >> # Step 0 to 6000: very fast heating
> > >> # Step 60001 to 160000: slow cooling
> > >> # Step 160001 to 180000: faster cooling
> > >> # Step 180000 to 200000: very fast cooling
> > >> &wt
> > >> type='TAUTP', istep1=0, istep2=60000,
> > >> value1=0.05, value2=0.05,
> > >> &end
> > >> &wt
> > >> type='TAUTP', istep1=60001, istep2=160000,
> > >> value1=1.0, value2=1.0,
> > >> &end
> > >> &wt
> > >> type='TAUTP', istep1=160001, istep2=180000,
> > >> value1=0.5, value2=0.5,
> > >> $end
> > >> &wt
> > >> type='TAUTP', istep1=180001, istep2=200000,
> > >> value1=0.05, value2=0.05,
> > >> &end
> > >> &wt
> > >> type='END',
> > >> &END
> > >> /
> > >>
> > >> _____________________________________________________
> > >>
> > >>
> > >> OUTPUT RUN-1
> > >>
> > >> NSTEP = 500 TIME(PS) = 50.250 TEMP(K) = 310.73 PRESS =
> > >> 0.0
> > >> Etot = -10363.4854 EKtot = 7777.7343 EPtot =
> > >> -18141.2197
> > >> BOND = 1916.0569 ANGLE = 4459.8222 DIHED =
> > >> 6585.8885
> > >> 1-4 NB = 2179.8858 1-4 EEL = 20755.1795 VDWAALS =
> > >> -5485.6124
> > >> EELEC = -42119.8223 EGB = -8122.6770 RESTRAINT =
> > >> 1690.0591
> > >> EAMBER (non-restraint) = -19831.2788
> > >>
> >
> ---------------------------------------------------------------------------
> > >> ---
> > >>
> > >> OUTPUT RUN-2
> > >>
> > >> NSTEP = 500 TIME(PS) = 50.250 TEMP(K) = 310.73 PRESS
> =
> > >> 0.0
> > >> Etot = -10363.4854 EKtot = 7777.7343 EPtot =
> > >> -18141.2197
> > >> BOND = 1916.0569 ANGLE = 4459.8222 DIHED =
> > >> 6585.8885
> > >> 1-4 NB = 2179.8858 1-4 EEL = 20755.1795 VDWAALS =
> > >> -5485.6124
> > >> EELEC = -42119.8223 EGB = -8122.6770 RESTRAINT =
> > >> 1690.0591
> > >> EAMBER (non-restraint) = -19831.2788
> > >>
> >
> ---------------------------------------------------------------------------
> > >> ---
> > >>
> > >>
> > >>
> > >> Many thanks in advance for your useful comments and help.
> > >>
> > >> thanks,
> > >> Ibrahim
> > >>
> > >>
> > >>
> > >> _______________________________________________
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> > >>
> > >
> >
> >
> >
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