AMBER Archive (2009)

Subject: Re: [AMBER] CCL4 simulation

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Mar 18 2009 - 06:06:30 CDT

On Wed, Mar 18, 2009, sudipta wrote:

> The bond energy and electrostatic
> energy were showing NAN, bend and vdw interaction energies were showing some
> value.

Is this in your starting structure? Once you get a NaN, everything
beyond that is toast. The usual problem is that you have two atoms on
top of each other, although that doesn't really explain what you are
seeing.

> I have placed the CCL4 molecules in a FCC lattice.

Ideas:

Try some different method, e.g. solvating CCl4 in CCl4 using the
solvateBox command. Run a few steps of minimization with ntpr=1; use
the checkoverlap command in ptraj to look for bad contacts.

...dac

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