[gmx-users] Another boring imaging question

[Berk Hess]

>From: david.evans at ulsop.ac.uk
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>Subject: [gmx-users] Another boring imaging question
>Date: Wed, 14 Jul 2004 12:09:58 +0100
>
>Dear all,
>
>The coordinates in the .tpr file generated by grompp (extractable via
>editconf) are different from those input in to grompp in the .gro file
>
>i.e.
>grompp -v -f md_equil.mdp -c input.gro -p input.top -norenum -o
>md_equil.tpr
>editconf -f md_equil.tpr -o output.gro
>
>results in files input.gro, output.gro which are different. In my
>particular case, output.gro has my DNA duplex split in half across
>the box.
>Is there a reason for this, or can I stop it? :) It messes up the
>trjconv -nojump option.

This is very strange.
As far as I know grompp and editconf (unless you use -pbc) do
not do anything to the pbc. And with the options you used
should not touch the coordinates at all and they gro files
should be identical (except maybe for generated velocities).

If you can easily give me access to the files I would like to
have a look at it.

But with trjconv you can use your gro file with -s to make
the -nojump option work as you want.

Berk.

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