if you look at the water box, do you see a depression (i.e. absence of
water) roughly in the shape of the part of your protein that is "out of the
box"? If so, this is just an imaging issue with periodic conditions, and
doesn't mean anything (i.e. it's what should happen).
There are commands in ptraj for re-centering the periodic box around
whatever you want (your one oligomer for instance).
~Aron
On Tue, Dec 11, 2012 at 5:42 PM, Ismail, Mohd F. <farid.ou.edu> wrote:
> I have a simulation of 4 oligomers in a box of water. What puzzles me is,
> when I looked at the pdb file of the restart file (min1.pdb), it shows all
> 4 of the oligomers within the box of water. But when I looked at the first
> trajectory produced (eq1a.pdb), it shows that some part of the oligomers
> are outside the water box. Can someone tell me what I did wrong?
>
> I made sure the input coordinate of the MD run to be the restrt file of
> the minimization run. Here is the snippet from the MD run:
> -------------------------------------------------------
> Amber 11 SANDER 2010
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 11
>
> | Run on 12/11/2012 at 16:15:00
>
> File Assignments:
> | MDIN: eq1a.inp
> | MDOUT: mdout.eq1a
> | INPCRD: restrt.min1a
> | PARM: oligo-water.prmtop
> | RESTRT: restrt.eq1a
> | REFC: refc
>
> The INPCRD is shown to be the correct file, but I don't get how the
> structure of the first run is different.
>
> *******************************
> Mohd Farid Ismail
> Graduate Student
> Dept. of Chemistry/Biochemistry
> University of Oklahoma
> Norman 73019
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Dec 11 2012 - 20:00:02 PST
