[gmx-users] Simple question (confout)

[Justin A. Lemkul]

On 6/15/12 12:11 PM, Dariush Mohammadyani wrote:
> Hi,
> Is there any difference between confout.gro file and last frame which we can
> extract from trajectory? I am thinking they are different!!
> When I see the trajectory I can see the edge of the well-shaped box, but when I
> see confout.gro it is not well-shaped and some atoms looks went out out of the box.

The confout.gro and last frame of a trajectory are the same, except for the fact 
that confout.gro has its molecules made whole for convenience.  That may result 
in some translation of molecules (apparent) positions.  You can prove this by 
using trjconv -dump to output the last frame of a trajectory and then use 
trjconv -pbc whole.  That result and confout.gro should be the same.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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