[gmx-users] Simple question (confout)
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 15 18:35:26 CEST 2012
On 6/15/12 12:11 PM, Dariush Mohammadyani wrote:
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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