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?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 26 2011 - 22:30:03 PDT
