[gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

[Visvaldas K.]

Thank you, Mark, for your tip, the indexing solution is perfect!
Regards,
Vis


--- On Tue, 12/22/09, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Tuesday, December 22, 2009, 7:29 PM
> Visvaldas K. wrote:
> > Dear GROMACS users and gurus,
> > 
> > I am sorry if it's a stupid question...I'm fairly new
> GROMACS, and something is been driving me crazy.  I
> have a protein, two metal ions, and inhibitor in my system.
> Somehow in some of the frames I can't keep all those pieces
> "clustered" compactly for some postprocessing,  using
> trjconv for conversion of trr/xtc into PDB format:
> > 
> > "-pbc mol" option of trjconv: metal ions are far from
> the rest of the protein.
> > -pbc nojump or -pbc whole: inhibitor far from the
> protein, metals are fine.
> > -pbc atom or -pbc res: couple of residues are
> disattached from the protein; metals and inhibitor are
> fine.
> > -pbc cluster: doesn't work (irrelevant?)
> 
> -pbc cluster should work with a suitable index group of
> protein+metal+inhibitor - that's what it is for.
> 
> Once that's done, you may want to re-run trjconv to apply
> other effects. Two-pass processing is often necessary.
> 
> > Also -center and -boxcenter don't seem to help...
> > Can anybody suggest some tricks? I used octahedral box
> for my runs.
> 
> "don't seem to help" also doesn't help. We can't guess what
> it was about your inputs and outputs that was contrary to
> your hopes :-)
> 
> Mark
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