AMBER Archive (2004)

Subject: Re: AMBER: solute leaving PBC box

From: Carlos Simmerling (
Date: Fri Oct 08 2004 - 09:02:42 CDT

the system is already imaged from iwrap,
however, if you want your solute in the MIDDLE
of the box, that is different from being imaged.
ptraj will allow you to center an your solute and
the reimage the solvent around it.
there is nothing wrong with your data, it is just a question
of how you want it to look visually.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:
=================================================================== wrote:

>So I have to run ptraj to image the system, even though iwrap was turned
>on? And even though the solute is sticking outside of the iwarped box,
>the molecule is still interacting with the solvent, thereby the
>simulation is still correct?
>Yes, you are right dt=0.001, I just typed the input on my windows machine
>instead of copying it over from the unix workstation.
>==============Original message text===============
>On Thu, 07 Oct 2004 17:43:49 EST Carlos Simmerling wrote:
>with iwrap, the molecule will be translated, but part of the molecule
>may still move outside the box before the whole molecule gets
>translated. this translation happens when the center of the molecule
>moves out of the box (see subroutine wrap_molecules in ew_box.f).
>in the future, you should send actual input files, since I doubt that
>you really
>ran with dt=0.01 (10fs), and there is no "tmp0", etc. it's very hard
>to help people when what they say they did is not what they really did.
>>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,
>>>ntb=2, ntp=1, pres0=1, taup=1.0
>>>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,
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