[gmx-users] Re: Re: problems with some calculated trajectories

[Berk Hess]

> Date: Thu, 25 Jun 2009 18:39:53 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: Re: problems with some calculated trajectories
> 
> Bernhard Knapp wrote:
> > 1) trjconv with the "-pbc nojump" option does not help - it removes most 
> 
> If I understand correctly, -pbc nojump will help when the relevant atoms 
> are part of the same [moleculetype]. One fragment in each of your two 
> examples is apparently the same four-strand sheet with helix wrapped 
> around it. This suggests to me that you might have several chains, each 
> as a different [moleculetype] and your observations are actually what 
> you should expect. If so, -pbc cluster is the kind of thing you should 
> be using.
> 

You did not understand correctly :)
-pbc nojump removes periodic jumps of atoms, it does not now about molecules.
The effect is that no periodic jumps occur from the reference structure
(either tpr or first frame). This means, for instance, that protein complexes
will stay intact and that water will diffuse out of the box in visualization.

Berk

> In any case, a description of the composition of your system and copies 
> of a series of commands that reproduces your result would always have 
> been appropriate :-)
> 
> Mark
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