failure of minimization

From: Ioana Cozmuta <>
Date: Fri, 21 Feb 2003 17:10:37 -0800 (PST)


I have a box of ionic solution (KCl, 44 ions and about 1700 water
molecules, size of 40A). I did build this in Leap with some initial random
coordinates of the ions (something I thoughth was ok as I was expecting the minimizer
would be able to handle).

Here is my input file:

Minimization of the KCl cell
   imin = 1, maxcyc = 500, ncyc = 200
   ntpr = 1, ntx = 1
   scnb = 2.0
   scee = 1.2
   ntf = 1, ntc = 1, igb = 0
   ntr = 1
   cut = 12.00
   ntc = 1
Group input for restrained atoms
RES 1 1756

I get the following message:

***** Processor 1 ***** System must be very
inhomogeneous. ***** Readjusting recip sizes. END In this slab, Atoms
found: 5180 Allocated: 3885

Initially my non-bonded energies are not a number but the minimizer seems
to be able to handle the vdw (it is reduced to -24.6510). However the
electrostatic energy remains NaN.

If I load the same initial structure in Cerius2 (accelrys software) and I
perform a minimization there, indeed I have a maximum force in the system
of about 10^20 kcal/mol/A and the energy component due to stress in the
order of 10^19kcal/mol. However after 500 steps of minimization I get
reasonable values (negative energies and max force ~10^1).

I would appreciate any suggestions on this.

Thank you in advance,
Received on Sat Feb 22 2003 - 01:53:00 PST
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