Re: [AMBER] Imaging issue

From: David A Case <>
Date: Tue, 8 Oct 2019 07:49:53 -0400

On Tue, Oct 08, 2019, Hira Jabeen wrote:

>The system has extended beyond
>     the extent of the virtual box.

This message arises when you are running a non-periodic simulation
(ntb=0) but sander is placing a pseduo-box (aka virual box) around the
system; then the system is moving outside that box.

Since you don't "really" have a periodic system, the image commands in
cpptraj are really not appropriate here. Try setting igb=6 in your
sander run (that avoids using a vitual box). And, of course, run a
short simulation, saving trajectory frames frequently, the visualizing
what is happening. Such visualization will often provide key hints
about what is happening.

...good luck...dac

p.s.: of course, if you really have a periodic system, then fix your
sander inputs to make sure that ntb is set to 1.

AMBER mailing list
Received on Tue Oct 08 2019 - 05:00:02 PDT
Custom Search