AMBER Archive (2002)

Subject: Re: md failure: deep energetics problem

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 05 2002 - 13:55:40 CST

On Thu, Dec 05, 2002, eric hu wrote:

> I'm doing a constrained md on a crystal structure
> docked with a ligand. It gives an error message below.
> I'm just curious what the deep problem might be.
>
> Eric
> md.in############################
> &cntrl
> imin=0,
> ntc=3, ntf=3,
> cut=12.0,
> ntpr=50,ntwx=50
> nstlim = 500000, dt=0.002,
> ntt=1, tempi=0.0, temp0=298.0, tautp=1.0,
> ntx=5, irest=1, ntb=0,ntr=1
> nscm = 1000,
> &end
> freeze residue 5TS
> 500
> RES 219
> End of md.out#########################
> vlimit exceeded for step 371691 ; vmax =
> 24.0104829598298
> vlimit exceeded for step 371696 ; vmax =
> 23.6314819228428
>
> Coordinate resetting (SHAKE) cannot be
> accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 1651 3344
> 3355
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>

It looks like it may be a problem with your restraints: 500 kcal/mol-A**2
is a *very* large force constant (esp. with dt=0.002). Are atoms 3344 and
3355 in resiude 219 (or otherwise inside the restainted group)? If nothing
else looks wrong with the structures, consider reducing the force constant
by about a factor of 50 -- that will still keep the atoms very close to their
starting positions, but will yeild more stable dynamics.

As usual, looking for other problems in the energies or geometries is also
recommended when you get a SHAKE failure.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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