[gmx-users] Protein out of the box (not PBC problem)

Mark Abraham mark.abraham at anu.edu.au
Fri Sep 10 11:23:21 CEST 2010

----- Original Message -----
From: Carla Jamous <carlajamous at gmail.com>
Date: Friday, September 10, 2010 19:15
Subject: [gmx-users] Protein out of the box (not PBC problem)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi everyone,
> please I can't figure out how to do this:
> I have a trajectory with water. If I concatenate it, since I have a FAT32 file system, it's a file too large! So I'm trying to avoid this.
> For that, I extracted my protein (it's a dimer) from each step of my simulation (when doing that, I did -pbc nojump and then I fit) and then concatenated all the steps, to obtain the whole trajectory with only the protein. When I watch my trajectory with VMD, I suspect that the distance between the monomers is larger than the dimension of my box.
>  I'm sure that it's not a PBC problem, because I already did trjconv -pbc nojump. 
> So my question is: is there a way to check if my protein is coming out of the box, without having to watch the whole trajectory with water molecules, because I can't do that.

If you still have a box defined, then VMD can show that. Open the Tk console and enter "pbc box". You can also get VMD to show some periodic images - probably in the Representations.

Maybe you want -center, or -fit progressive at some stage. trjconv has a million options... something will probably render things how you'd like them :-) Check out trjconv -h, of course.


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