What do you mean by "messy"? Are they still not in the box? Are you
using VMD and the molecules appear distorted? If it's the latter you
are probably not reading the trajectory in as "coordinates with
periodic boundaries". The input you provided should work for most
systems.
-Dan
On Tue, Jul 5, 2016 at 5:25 AM, Ming Tang <m21.tang.qut.edu.au> wrote:
> Dear list,
>
> I did a NPT study without setting iwrap=1, and find that water molecules are not in the box. From the archive I learnt that I can translate molecules back to the primary box using cpptraj. I tried the following command but found that the water molecules in the trajectory file are still messy.
>
> trajin test.mdcrd
> autoimage
> trajout test1.mdcrd
>
> is my command correct??
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jul 05 2016 - 05:00:02 PDT
