AMBER Archive (2004)

Subject: Re: AMBER: unformatted md problem

From: David A. Case (
Date: Mon Sep 27 2004 - 10:06:05 CDT

On Mon, Sep 27, 2004, richard dimelow wrote:

> I'm having a problem with a molecular dynamics run in sander.
> The coordinates and velocities are read unformatted (ntx=4), i am not using
> periodic boundary conditions (ntb=0) and i am not using the generalised born
> model (igb=0). When doing this the following error message appears in the
> output
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> Cannot read unformatted coord for nonperiodic system
> For ntb=0, ntx must be 1,5,7,9

When doing a simulation with ntb=0 and egb=0, the program sets up a
pseudo-box, which is used to construct the non-bonded list. Hence, certain
code paths through the "ewald" section of code are taken.

GB simulations do not use a non-bonded list (currently), so this does not


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