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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Received on Fri Feb 27 2009 - 01:10:28 PST
