Hi,
Currently neither ptraj or cpptraj perform imaging during hydrogen
bond analysis due to the sheer number of distances that are typically
calculated. The idea is that users will perform imaging (with 'image'
in ptraj or 'autoimage' in cpptraj) prior to the hbond command. If
both of your chain ends are outside your periodic box then hydrogen
bonds between the ends will not be calculated. However, unless you're
supposed to have such a high concentration of your solute you may want
to consider increasing the size of your unit cell, otherwise you will
get strong interactions between images of your system that you
probably don't want.
-Dan
On Fri, Apr 12, 2013 at 10:20 PM, Binwu Zhao <bzhao.ncsu.edu> wrote:
> Dear Amber Users:
>
> I've been using NPT ensemble to run a long polypeptides, then after
> centering the water to the "primary box", I found that both my chain ends
> are out of the box. My concern is whether the hydrogen bonds calculation
> will accurately reflect the really number of hydrogen bonds, since I'm
> analyzing the post trajectory with water already centered.
> If not, will the only thing I can do is to increase my buffer to a much
> larger number and rerun the simulation? I'm not sure whether ptraj or
> cpptraj will consider the constant pressure and volume change when they are
> doing the analysis? Or do they just use the water in the primary box to
> calculate it?
> Thanks!
>
> Binwu
>
> --
> Binwu Zhao
> Dept of Chemical and Biomolecular Engineerig
> NCSU
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Apr 15 2013 - 07:30:04 PDT
