Re: [AMBER] Model building

From: Aparna P <aparnaspap.gmail.com>
Date: Tue, 27 Sep 2011 10:31:58 +0530

Sir

My MD inputs are

*MD 1.in*


DNA 10ps MD with res 10 kcal/mol
restraints
 &cntrl

  imin =
0,
  irest =
0,
  ntx =
1,
  ntb =
1,
  cut =
10,
  ntr =
1,
  ntc =
2,
  ntf =
2,
  tempi =
0.0,
  temp0 =
150.0,
  ntt =
3,
  gamma_ln =
1,
  nstlim = 50000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr =
1000,
  nmropt =
1,
 /

 &wt type = 'TEMP0', istep1 = 0, istep2 = 25000, value1 = 0.0, value2 =
150.0,
 /

 &wt type =
'END'
 /

Keep YDNA fixed with weak
restraints
10.0

RES 1
20
END

END


*MD2.in*

DNA : 10ps MD with res 10 kcal at const
volume
 &cntrl

  imin =
0,
  irest =
1,
  ntx =
5,
  ntb =
1,
  cut =
10,
  ntr =
1,
  ntc =
2,
  ntf =
2,
  tempi =
145.83,
  temp0 =
300.0,
  ntt =
3,
  gamma_ln =
1,
  nstlim = 50000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr =
1000,
  nmropt =
1,
 /

 &wt

  type = 'TEMP0', istep1 = 1, istep2 =25000, value1 = 145.83, value2 =
300.0,
 /

 &wt


type='END'

 /



Group Input for restrained
atoms
10.0

RES 1
20
END

END


*MD3.in*

DNA: 50ps MD with res on complex 5 kcal constant
pressure
 &cntrl

  imin =
0,
  irest =
1,
  ntx =
5,
  ntb = 2, pres0 =1.0,
ntp=1,
  cut =
10,
  ntr =
1,
  ntc =
2,
  ntf =
2,
  tempi =
295.47,
  temp0 =
300.0,
  ntt =
3,
  gamma_ln =
1,
  nstlim = 50000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr =
1000,
  nmropt =
1,
 /



 &wt

  type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 295.47, value2 =
300.0,
 /

 &wt

 type = 'TEMP0', istep1 = 2001, istep2 = 25000, value1 = 300.0, value2 =
300.0
 /

 &wt


type='END'

 /



Group Input for restrained
atoms
5.0

RES 1
20
END

END


*MD4.in*

YDNA: 50ps MD with res 2 kcal constant
pressure
 &cntrl

  imin =
0,
  irest =
1,
  ntx =
5,
  ntb = 2, pres0 = 1.0, ntp
=1,
  cut =
10,
  ntr =
1,
  ntc =
2,
  ntf =
2,
  tempi =
300.0,
  temp0 =
300.0,
  ntt =
3,
  gamma_ln =
1,
  nstlim = 50000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr =
1000,
  nmropt =
1,
 /

 &wt

  type = 'TEMP0', istep1 = 1, istep2 = 25000, value1 = 300.0, value2 =
300.0,
 /

 &wt


type='END'

 /



Group Input for restrained
atoms
2.0

RES 1
20
END

END


*MD5.in*

DNA: 50ps MD with res 1 kcal constant
pressure
 &cntrl

  imin =
0,
  irest =
1,
  ntx =
5,
  ntb = 2, pres0 = 1.0, ntp =
1,
  cut =
10,
  ntr =
1,
  ntc =
2,
  ntf =
2,
  tempi =
300.0,
  temp0 =
300.0,
  ntt =
3,
  gamma_ln=
1,
  nstlim = 50000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr =
1000,
  nmropt =
1,
 /

 &wt

  type = 'TEMP0', istep1 = 1, istep2 = 25000, value1 = 300.0, value2 =
300.0,
 /

 &wt


type='END'

 /



Group Input for restrained
atoms
1.0

RES 1
20
END

END

*MD6.in*

DNA: 50ps MD with res 0.5 kcal constant
pressure
 &cntrl

  imin =
0,
  irest =
1,
  ntx =
5,
  ntb = 2, ntp = 1, pres0 =
1.0,
  cut =
10,
  ntr =
1,
  ntc =
2,
  ntf =
2,
  tempi =
300.0,
  temp0 =
300.0,
  ntt =
3,
  gamma_ln=
1,
  nstlim = 50000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr =
1000,
  nmropt =
1,
 /

 &wt

  type = 'TEMP0', istep1 = 1, istep2 =25000, value1 = 300.0, value2 =
300.0,
 /

 &wt


type='END'

 /



Group Input for restrained
atoms
0.5

RES 1
20
END

END

*MD7.in*

DNA: 50ps MD with res 0.1 kcal constant
pressure
 &cntrl

  imin =
0,
  irest =
1,
  ntx =
5,
  ntb = 2, ntp = 1, pres0 =
1.0,
  cut =
10,
  ntr =
1,
  ntc =
2,
  ntf =
2,
  tempi =
300.0,
  temp0 =
300.0,
  ntt =
3,
  gamma_ln =
1,
  nstlim = 50000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr =
1000,
  nmropt =
1,
 /

 &wt

  type = 'TEMP0', istep1 = 1, istep2 =25000, value1 = 300.0, value2 =
300.0,
 /

 &wt


type='END'

 /



Group Input for restrained
atoms
0.1

RES 1
20
END

END

*MD8.in*

DNA: 50ps MD with res 0.01 kcal constant
pressure
 &cntrl

  imin =
0,
  irest =
1,
  ntx =
5,
  ntb = 2, ntp = 1, pres0 =
1.0,
  cut =
10,
  ntr =
1,
  ntc =
2,
  ntf =
2,
  tempi =
300.0,
  temp0 =
300.0,
  ntt =
3,
  gamma_ln =
1,
  nstlim = 50000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr =
1000,
  nmropt =
1,
 /

 &wt

  type = 'TEMP0', istep1 = 1, istep2 =25000, value1 = 300.0, value2 =
300.0,
 /

 &wt


type='END'

 /



Group Input for restrained
atoms
0.01

RES 1
20
END

END
*
MD9.in*

DNA: 200ps MD (production run in
NPT)
 &cntrl

  imin =
0,
  irest =
1,
  ntx =
5,
  ntb = 2, ntp = 1, pres0 =
1.0,
  cut =
10,
  ntr =
0,
  ntc =
2,
  ntf =
2,
  tempi =
300.0,
  temp0 =
300.0,
  ntt = 3, gamma_ln =
1,
  nstlim = 200000, dt =
0.001,
  ntpr = 500, ntwx = 500, ntwr = 1000,
  iwrap=1,
 /

Sir as your suggestion I have increased the minimisation steps.But still the
vlimit exeeding problem exists.
What can I do sir?
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Received on Mon Sep 26 2011 - 22:30:03 PDT
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