AMBER Archive (2007)

Subject: Re: AMBER: MD simulation error

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 24 2007 - 19:55:09 CDT

On Tue, Jul 24, 2007, Lili Peng wrote:
>
> I am getting the following error for my MD simulation:
>
> Coordinate resetting (SHAKE) cannot be accomplished, deviation
> is too large
>
>
> NITER, NIT, LL, I and J are : 0 1 7 16 28
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>
> My input file is the following:
>
> 310K constant temp MD
> &cntrl
> imin=0, ntb=1,
> cut=8.0, ntc=3, ntf=3,
> tempi=310.0, temp0=310.0,
> ntt=3, gamma_ln=50,
> nstlim=10000, dt=0.005,
> ntpr=1, ntwx=1,
> /
>
> Does anyone have any idea why this occurs? Does it have anything to do with
> the timestep?

Very likely. A fs time step is much too big for ordinary simulations. Why
don't you use the default value of 0.001?

(Again, to everyone: one the best ways to learn is to experiment! You clearly
almost knew the answer to your question before sending the email. And, if
it turns out that something else is wrong with your system, trying different
values of dt will tell you that as well.)

...dac

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