[AMBER] vlimit error during equilibration step

From: Nicee <nicee.srivastava.imtech.res.in>
Date: Tue, 30 Mar 2010 10:07:28 +0530 (IST)

Hello,

I m running a simulation of a protein model with Amber10 and during second step
of equilibration im getting following error.

vlimit exceeded for step 1; vmax = 31.5574

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 489 980 981

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

Earlier i had minimized the protein for 500 steps. Then heated it gradually
during first equilibration at nvt with shake on hydrogen bonds and restrain on
protein with a force constant of 5kcal/mol A. Im attaching the input and output
file of this first equilibration.
Input for the first equilibration is:

Equilibration 1 with restraint on protein and constraint on hydrogen bonds
 &cntrl
  imin = 0, ntb = 1,
  igb = 0, ntpr = 2000, ntwx = 2000,
  iwrap=1,
  ntt = 3, gamma_ln = 1.0,
  tempi = 0,
  ntc=2, ntf=2,
  ntr=1, nmropt=1,
  nstlim = 600000, dt = 0.002,
  cut = 12.0

 &end
 &wt
  type='TEMP0', istep1=0, istep2=20000,
                value1=0, value2=10,
 &end
 &wt
  type='TEMP0', istep1=20001, istep2=40000,
                value1=11, value2=20,
 &end
 &wt
  type='TEMP0', istep1=40001, istep2=60000,
                value1=21, value2=30,
 &end
 &wt
  type='TEMP0', istep1=60001, istep2=80000,
                value1=31, value2=40,
 &end
 &wt
  type='TEMP0', istep1=80001, istep2=100000,
                value1=41, value2=50,
 &end
 &wt
  type='TEMP0', istep1=100001, istep2=120000,
                value1=51, value2=60,
 &end
 &wt
  type='TEMP0', istep1=120001, istep2=140000,
                value1=61, value2=70,
 &end
 &wt
  type='TEMP0', istep1=140001, istep2=160000,
                value1=71, value2=80,
 &end
 &wt
  type='TEMP0', istep1=160001, istep2=180000,
                value1=81, value2=90,
 &end
 &wt
  type='TEMP0', istep1=180001, istep2=200000,
                value1=91, value2=100,
 &end
 &wt
  type='TEMP0', istep1=200001, istep2=220000,
                value1=101, value2=110,
 &end
 &wt
  type='TEMP0', istep1=220001, istep2=240000,
                value1=111, value2=120,
 &end
 &wt
  type='TEMP0', istep1=240001, istep2=260000,
                value1=121, value2=130,
 &end
 &wt
  type='TEMP0', istep1=260001, istep2=280000,
                value1=131, value2=140,
 &end
 &wt
  type='TEMP0', istep1=280001, istep2=300000,
                value1=141, value2=150,
 &end
 &wt
  type='TEMP0', istep1=300001, istep2=320000,
                value1=151, value2=160
 &end
 &wt
   type='TEMP0', istep1=320001, istep2=340000,
                value1=161, value2=170
 &end
 &wt
  type='TEMP0', istep1=340001, istep2=360000,
                value1=171, value2=180,
 &end
 &wt
  type='TEMP0', istep1=360001, istep2=380000,
                value1=181, value2=190,
 &end
 &wt
  type='TEMP0', istep1=380001, istep2=400000,
                value1=191, value2=200,
 &end
 &wt
  type='TEMP0', istep1=400001, istep2=420000,
                value1=201, value2=210,
 &end
 &wt
  type='TEMP0', istep1=420001, istep2=440000,
                value1=211, value2=220
 &end
 &wt
  type='TEMP0', istep1=440001, istep2=460000,
                value1=221, value2=230,
 &end
 &wt
  type='TEMP0', istep1=460001, istep2=480000,
                value1=231, value2=240,
 &end
 &wt
  type='TEMP0', istep1=480001, istep2=500000,
                value1=241, value2=250,
 &end
 &wt
  type='TEMP0', istep1=500001, istep2=520000,
                value1=251, value2=260,
 &end
 &wt
  type='TEMP0', istep1=520001, istep2=540000,
                value1=261, value2=270
 &end
 &wt
  type='TEMP0', istep1=540001, istep2=560000,
                value1=271, value2=280,
 &end
 &wt
  type='TEMP0', istep1=560001, istep2=580000,
                value1=281, value2=290,
 &end
 &wt
  type='TEMP0', istep1=580001, istep2=600000,
                value1=291, value2=300,
 &end
 &wt
  type='END'
/
HOLD THE PROTEIN FIXED
5.0
RES 1 306
END
END

It went fine. Next i wanted to decrease the force constant gradually keeping the
temperature constant. I had planed out different equilibration steps with
decreasing the force constant to 2.5, 1.0, 0.0 for every 200000 steps,keeping
temperature constant, nvt ensemble, and shake constrain on hydrogen bonds. But
the second equilibration didnt even started and ended up with the above error.

The input file for second equilibration is:

Equilibration 2 with decreasing restraint on protein and constraint on hydrogen
bonds
 &cntrl
  imin = 0, ntb = 1,
  igb = 0, ntpr = 2000, ntwx = 2000,
  iwrap=1,
  irest=1,ntx=5,
  ntt = 3, gamma_ln = 1.0,
  tempi = 300, temp0=300,
  ntc=2, ntf=2,
  ntr=1,
  nstlim = 200000, dt = 0.002,
  cut = 12
/
HOLD THE PROTEIN FIXED
2.5
RES 1 306
END
END

Does this problem has anything to do with shake, should i not use it. Or does it
has anything to do with ntt=3, should i use berendsen method with ntt=1( Im
really confused with this ).Is this way of giving restraint is fine or should i
use resatrain_mask and restarin_wt. Can the problem be due to the cut off,
should I decrease it. Kindly help with the problem n suggest something.

One more thing, on visualizing the protein after first equilibration on VMD it
was observed that protein was coming out of the water box starting from the
first step.However, it was well within the water box at the end of minimization.
How and why did this happened. Kindly explain.

Thanking you.

Nicee.



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Received on Mon Mar 29 2010 - 22:00:04 PDT
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