AMBER Archive (2004)

Subject: Re: AMBER: solute leaving PBC box

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Oct 07 2004 - 16:48:12 CDT

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.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

opitz_at_che.udel.edu wrote:

>Dear Amber Community,
>
>I am running MD in a periodic box, with the following input:
>&cntrl
> 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
>&end
>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,
>
>Armin
>
>
>
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