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.abra...@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.kr...@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.ne...@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-boun...@maillist.sys.kth.se < > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > > > Abraham <mark.j.abra...@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.ne...@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. > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? 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