[gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

[Kroon, P.C.]

Alternatively, center it on an interfacial residue. pbc cluster doesn't
always work, unfortunately.

Peter

On Sat, Feb 4, 2017 at 7:56 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> Awesome Mark, thanks! It works.
>
> I filed a bug about a nonexistent -clustercenter option mentioned in the
> v5.1.2 help file, but the command seems to work anyway for my usage.
>
> Thanks again,
> Chris.
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: 04 February 2017 07:27:52
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] how to reimage PBC based on distance to a given
> selection without recentering or otherwise changing atomic coordinates
>
> Hi,
>
> I've never really use it myself, but I imagine trjconv -pbc cluster is
> useful for this kind of scenario when you want to treat a group of
> molecules as indivisible.
>
> Mark
>
> On Sat, 4 Feb 2017 09:33 Christopher Neale <chris.neale at alum.utoronto.ca>
> wrote:
>
> > Dear users:
> >
> > I have a system in which molecule A is in direct contact with molecule B.
> > However, molecule B is imaged in a different periodic cell. What I would
> > like to do is to get an image of both molecules in a periodic
> > representation in which they actually are in contact (i.e., reimage
> > molecule B such that it is closest to molecule A). However, I do not want
> > to lose spatial information with e.g. a trjconv -center -pbc mol command.
> >
> > This is part of a complex automated build procedure and I can get into
> > more details if that is useful, but the crux is that I am extracting a
> > frame from a simulation, building more atoms onto molecule A, and setting
> > up a new simulation. To build onto molecule A, I want to then do a vacuum
> > EM before adding it back to the water box, for which I first enlarge the
> > vacuum box, and changing box dimensions is messing with the periodicity
> and
> > throwing molecule B away from molecule A in an unrealistic fashion
> > (molecule B is a tightly bound ligand).
> >
> > I could do what I want by breaking each molecule out into its own box,
> > checking for contacts, reimaging, and then putting them back together. I
> > presume (but have not checked) that I could also do this by making a new
> > .itp file in which both molecule A and B are part of the same [ molecule
> ]
> > definition and then running a zero-step mdrun. However, I am writing to
> see
> > if anybody knows how reimage based on a selection (would be a single atom
> > in molecule A near the contact between molecule A and B) more elegantly
> > with processing tools available in gromacs.
> >
> > Thank you for your help,
> > Chris.
> > --
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