Re: [AMBER] about ewald error estimate

From: Navanath Kumbhar <nmkumbhar.gmail.com>
Date: Tue, 8 Jun 2010 22:26:53 +0530

Dear sir,

Thank you for your early reply, i have made changes in my input files and
run after equilibration, i got same error as like of that previous: Ewald
error estimate: 0.4278E-04

My input file is here,

100ps of md
&cntrl
imin=0,
irest=1,
ntx=7,
ntb=2,
pres0=1,
ntp=1,
taup=0.2,
cut=10,
ntr=0,
ntc=2,
ntf=2,
tempi=300.0,
temp0=300.0,
ntt=3,
gamma_ln=1.0,
nstlim=50000, dt=0.002,
ntpr=500, ntwx=500, ntwr=10000
/

I have attached output file for this input.

So please see and give me suggestion to solve this problem.

Thanks and great regards
from
Navanth Kumbhar

n Mon, Jun 7, 2010 at 5:42 PM, case <case.biomaps.rutgers.edu> wrote:

> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Tue Jun 08 2010 - 10:00:04 PDT
Custom Search