AMBER Archive (2008)

Subject: Re: AMBER: equilibration

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Oct 21 2008 - 06:01:54 CDT

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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