Hi,
You still have not performed any minimization, imin = 1 (at least not
according to any of the input you have posted). Prior to running any
MD you should run minimization (I would say at least 1000 steps) to
allow your system to relax. If your system starts with bad contacts
(overlapping VDW radii, two like charges in close proximity etc) this
can generate large initial forces which will kill the run after a
couple of steps.
Also, in my opinion there's no need to gradually bring your system up
to your target temperature using 'nmropt' and weight-changes. Just set
tempi and temp0 equal to your target temperature and let a random
velocity distribution be chosen (which is done when irest = 0).
Last, I recommend you set ig = -1 so that the random-number generator
is seeded properly, for both the initial velocity distribution and the
Langevin thermostat.
-Dan
On Tue, Sep 27, 2011 at 1:01 AM, Aparna P <aparnaspap.gmail.com> wrote:
> 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 Tue Sep 27 2011 - 05:00:02 PDT
