AMBER Archive (2007)

Subject: Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9)

From: David A. Case (case_at_scripps.edu)
Date: Fri Mar 16 2007 - 14:51:14 CST

On Wed, Mar 14, 2007, Eric Shamay wrote:

> I've had no success in running through a minimization of a system of water
> and nitric acid molecules. 2670 atoms in a 30x30x30 cubic periodic box.
>
>
> as I've got no
> overlaps of atoms, and I've checked out the force field parameters and they
> seem kosher.

>From your output:

 
   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 4.1709E+11 1.5809E+11 7.2311E+12 O 2500

 BOND = 356.6873 ANGLE = 51.5459 DIHED = 0.0092
 VDWAALS = ************* EEL = 193.2689 HBOND = 0.0000
 1-4 VDW = 0.0000 1-4 EEL = -6143.6685 RESTRAINT = 0.0000

 
   NSTEP ENERGY RMS GMAX NAME NUMBER
    250 -4.0319E+06 3.9172E+09 1.8545E+11 H 559

 BOND = 369.8618 ANGLE = 563.6761 DIHED = 184.9566
 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000
 1-4 VDW = 0.0000 1-4 EEL = -4029233.7698 RESTRAINT = 0.0000

 
   NSTEP ENERGY RMS GMAX NAME NUMBER
    500 -5.1727E+07 6.4765E+11 3.0661E+13 H 559

 BOND = 369.8611 ANGLE = 563.6750 DIHED = 184.9566
 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000
 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000

It looks like your are getting 1-4 interactions on top of one another. I note
that you have 1-4 EEL terms but no 1-4 VDW terms. This sounds like you have
pairs of atoms (probably atom 559 connecting with another atom) that have no
vDW interactions and hence get very close, leading to extremely large and
negative 1-4 EEL terms. Stop the simulation after 500 steps and use the
checkoverlap command in ptraj to analyze the system. (Or use some other
method: this should not be that hard to localize).

...good luck...dac

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