hi
your all input files are ok all are running fine.
To solve the problem you should download prmtop and inpcrd file from tutorial
and rerun it. Then
compare your all process from starting what you are doing e.g. from generation
of model onwords with tutorial.
> sir
>
> I have done two steps of minimisations.
> *min1.in*
>
> BDNA initial minimisation solvent +
> ions
> &cntrl
>
> imin =
> 1,
> maxcyc =
> 1000,
> ncyc =
> 500,
> ntb =
> 1,
> ntr =
> 1,
> cut =
> 10
> /
>
> Hold the complex
> fixed
> 500.0
>
> RES 1
> 20
> END
>
> END
>
> *min2.in*
>
> BDNA initial minimisation whole
> system
> &cntrl
>
> imin =
> 1,
> maxcyc =
> 5000,
> ncyc =
> 1000,
> ntb =
> 1,
> ntr =
> 0,
> cut =
> 10
> /
>
>
> and after this as you suggested
> "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."
>
> BDNA 50 ps 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 =
> 300.0,
> temp0 =
> 300.0,
> ntt =
> 3,
> gamma_ln =
> 1,
> nstlim = 25000, dt =
> 0.002,
> ntpr = 500, ntwx = 500, ntwr =
> 1000,
> nmropt = 0,
> ig =
> -1,
>
> /
>
> Keep BDNA fixed with weak
> restraints
> 10.0
>
> RES 1
> 20
> END
>
> END
>
>
> The programme got stopped at the beginning itself. It showed the error
>
> NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 245.01 PRESS =
> 0.0
> Etot = -39897.9725 EKtot = 6227.9688 EPtot =
> -46125.9413
> BOND = 161.3425 ANGLE = 751.0259 DIHED =
> 608.2930
> 1-4 NB = 267.8658 1-4 EEL = -5554.0864 VDWAALS =
> 5996.5543
> EELEC = -48505.1786 EHBOND = 0.0000 RESTRAINT =
> 148.2422
> EAMBER (non-restraint) = -46274.1835
> Ewald error estimate: 0.1792E-04
> ------------------------------------------------------------------------------
>
>
> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 274.13 PRESS =
> 0.0
> Etot = -37950.8556 EKtot = 6968.2052 EPtot =
> -44919.0607
> BOND = 184.9061 ANGLE = 748.3211 DIHED =
> 641.1166
> 1-4 NB = 271.7571 1-4 EEL = -5544.9752 VDWAALS =
> 5422.4565
> EELEC = -46785.0137 EHBOND = 0.0000 RESTRAINT =
> 142.3708
> EAMBER (non-restraint) = -45061.4315
> Ewald error estimate: 0.6601E-04
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 1376; vmax = 69.4332
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 211 585 586
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> sir can you suggest an input file for this system? (modelled DNA).
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 29 2011 - 11:00:03 PDT
