your initial restraint energies are very large- i suspect you are not using
the correct reference structure.
hard to say what's wrong with step 2 since you didn't provide the output.
On Tue, Mar 30, 2010 at 12:37 AM, Nicee <nicee.srivastava.imtech.res.in>wrote:
> 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 Tue Mar 30 2010 - 05:00:02 PDT
