AMBER Archive (2008)

Subject: Re: AMBER: equilibration

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Tue Oct 21 2008 - 06:28:17 CDT

I just checked it but also with ntr=0 error is the same

Urszula

> have you tried with ntr=0? that will help narrow down the source of
> the problem.
>
>
> On Tue, Oct 21, 2008 at 7:17 AM, Urszula Uciechowska
> <urszula.uciechowska_at_pharmazie.uni-halle.de> wrote:
> > yes the inpcrd is the same as the refc,
> > i changed the mask to restraintmask=':1-300_at_CA', restraint_wt=10
> > but the error is still the same:
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 0 68 4641 4639
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> >
> > Urszula
> >
> >
> >
> >> is the inpcrd the same as the refc?
> >> the mask looks odd- have you carefully checked the sander output to
> >> make sure it selects what you want?
> >>
> >>
> >> On Tue, Oct 21, 2008 at 6:44 AM, Urszula Uciechowska
> >> <urszula.uciechowska_at_pharmazie.uni-halle.de> wrote:
> >> > Dear amber users,
> >> >
> >> > I am trying to equilibrate the total volume of the water box for
> 20
> >> ps, at constant pressure (1atm) and
> >> > constant temperature (300K), and with positional restraints for CA
> >> and the crystal waters.
> >> > the input file:
> >> > &cntrl
> >> > imin = 0, irest = 0, ntx = 1,
> >> > ntb = 2, pres0 = 1.0, ntp = 1,
> >> > taup = 2.0,
> >> > cut = 9, ntr = 1,
> >> > ntc = 2, ntf = 2,
> >> > tempi = 300.0, temp0 = 300.0,
> >> > ntt = 3, gamma_ln = 1.0,
> >> > nstlim = 25000, dt = 0.002,
> >> > ntpr = 50, ntwx = 50, ntwr = 50
> >> > restraintmask=':1-300_at_CA&:4799-40288', restraint_wt=10
> >> > /
> >> > I am getting such a error:
> >> >
> >> > Coordinate resetting (SHAKE) cannot be accomplished,
> >> > deviation is too large
> >> > NITER, NIT, LL, I and J are : 0 0 68 4641 4639
> >> >
> >> > Note: This is usually a symptom of some deeper
> >> > problem with the energetics of the system.
> >> >
> >> > Could somebody help me to track the problem?
> >> >
> >> > Urszula
> >> >
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