AMBER Archive (2004)

Subject: Re: AMBER: solute leaving PBC box

Date: Thu Oct 07 2004 - 17:01:19 CDT

('binary' encoding is not supported, stored as-is) Sorry, I should have made my question clearer.
If iwarp is turned on, shouldn't the molecule be imaged back into the box
(even, if that means "breaking" up the molecule and have it come into the
box from different sides?). And based on that is the behavior of the
molecule affected by this or is it still ok?

Best Regards,


==============Original message text===============
On Thu, 07 Oct 2004 16:48:12 EST Carlos Simmerling wrote:

this is fine. you can use the image command in ptraj to
make it easier to view (center on the molecule of interest
and then image). check the ptraj documentation for details.

>Dear Amber Community,
>I am running MD in a periodic box, with the following input:
> imin=0, irest=1, ntx=5,
> iwrap=1,
> ntb=2, ntp=1, pres0=1, taup=1.0
> ntf=1,
> igb=0,
> ntr=0, cut=12,
> ntt=1, tempi=300, tmp0=300, tautp=1
> nstlim=2600000, dt=0.01, t=400,
> ntpr=1000, ntwx=1000, ntwr=1000
>At the end of this I took a look at my simulation, and my solute (the
>molecule of interest), has migrated through the box to one of its
>corners. Parts of the molecule are sticking out of the box, and aren't
>imaged back into the box.
>Does this affect the molecule behavior? If so how could i prevent it from
>leaving the box?
>Please help.
>Best Regards,

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to