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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.

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

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

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.

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

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