AMBER Archive (2009)

Subject: RE: [AMBER] Simulated annealing

From: Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)] (shaowen.hu-1_at_nasa.gov)
Date: Thu Feb 26 2009 - 10:22:59 CST

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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> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
>
>
>
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