AMBER Archive (2009)

Subject: Re: [AMBER] Simulated annealing

From: Ibrahim Moustafa (I.moustafa_at_psu.edu)
Date: Thu Feb 26 2009 - 09:28:44 CST

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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