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.
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Received on Tue Oct 08 2019 - 05:00:02 PDT
