AMBER Archive (2008)

Subject: Re: AMBER: equilibration

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Oct 21 2008 - 06:20:13 CDT

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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