On Mon, Jun 07, 2010, Navanath Kumbhar wrote:
>
> I have problem about ewald error estimate during equilibration run. So
> please tell me whether i am wrong in setting parameter for equilibration or
> have any problem in input file. I have created .prepin and frcmod file for
> modified nucleosides by using .gaff force field in antechamber. so it is
> write for performing equlibration md and production md.
>
> my input file for equlibration is here:
>
>
>
> imin=0, irest=0, ntx=1,
> ntb=1, cut=9.0, ntr=1,
> ntc=2, ntf=2, tempi=0.0, temp0=300.0,
> ntt=3, gamma_ln=1.0,
> nstlim=10000, dt=0.002,
> ntpr=250, ntwx=250,ntwr=10000
> /
> Keep DNA fixed with weak restraint
> 10.0
> RES 1 20
> END
> END
[Aside: your DNA constraints would qualify as "strong" or "very-strong", not
"weak". If you want a weak constraints, try a force constant of 0.1 or so.]
> *Ewald error estimate: 0.1498E-03*
If you look at sample outputs in the amber test suite (e.g. in the test/dhfr
subdirectory) you will find error estimates very similar to these...I don't
see any problem here.
....dac
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Received on Mon Jun 07 2010 - 05:30:03 PDT
