On Mon, Feb 29, 2016, necmettin pirinccioglu wrote:
>
>
> I have been running MD for diphosphoric acid anion with the following input
> but I get the error message below. Helps will be welcomed!
>
> INPUT
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=250000, dt=0.002,
> ntc=4, ntf=4,
> ntt=1, tautp=0.5,
> tempi=600.0, temp0=600.0,
> ntpr=500, ntwx=500,
> ntb=0, igb=0,
> cut=999
> /
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 1 1 2
It's hard to know what is wrong without more information. It is very likely
that at time step of 2 fs is too large at 600 K. The ntc=4 option is not
familiar to me, and I'm not sure what it will really do: try setting that to 2
or 3. Setting ntf=4 seems very dangerous: certainly consider running your
simulation with more standard parameters (and a more standard temperature)
first: that will help narrow down the causes of the problem.
What is the charge on your molecule? If you have hydrogens on phosphate
groups, you can get bad geometries unless you create the force field you are
using in a careful way. To debug, set nstlim to a fairly small number,
set ntpr and ntxw to 1, and look carefully at what happens to your structure
....dac
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Received on Mon Feb 29 2016 - 05:00:03 PST
