AMBER Archive (2003)

Subject: failure of minimization

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Feb 21 2003 - 19:10:37 CST

Hi,

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
&cntrl
   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
&end
Group input for restrained atoms
 1.0
RES 1 1756
END
END

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,
Ioana