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

[Kroon, P.C.]

Hi,

I don't have an example at hand, but I'll remember!
Thanks for the hard work :)

Peter

On Mon, Feb 6, 2017 at 10:08 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> If so, please share a case on https://redmine.gromacs.org that doesn't
> work
> as you think it should. We're very happy to make things work better!
>
> Mark
>
> On Mon, 6 Feb 2017 10:04 Kroon, P.C. <p.c.kroon at rug.nl> wrote:
>
> > 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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