Hi, It would be helpful to know if this is a known bug/issue. I'd rather not have to write code to recenter in this case -- would be easy if I just had one molecule far from the edges of the box but I am simulating a crowded system and need to get it centered on one complex within the system while still maintaining the cubic shape of the box -- I suppose I could write a script to pass atoms from one side of the box to the other as a result of the translation, but the box size slightly changes at each step (it's an NPT simulation) and I fear I'd be messing things up -- so I'd really rather not have to do that if there is actually a way with -center. I can't get anything to work the way the documentation says it's supposed to.
Does anyone out there know if this is a known bug? Any of the developers, perhaps? Thanks, Mala On Wed, Feb 6, 2019 at 9:30 AM Gyorgy Hantal <gyorgy.han...@univie.ac.at> wrote: > Hi, > > I also had that experience with trjconv with various versions. I ended up > doing the centering by a script. > I know on the other hand that centering works well in the case of for > example gmx density. Yet I've had no luck with trjconv... > Maybe this is known issue..? > > Regards, > Gyorgy > > On Tue, 5 Feb 2019 at 20:27, Mala L Radhakrishnan <mradh...@wellesley.edu> > wrote: > > > Hi again, > > > > As a follow up to my earlier email -- I added -pbc atom to the flags, > for a > > total command line of: > > > > gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tpr -b 201000 -e 201000 -n > > INDEX.ndx -pbc atom -center > > > > This brought it "closer" to the group I chose being centered, but it is > > still not centered at the geometric center of the group I chose. I'm > not > > sure why including -pbc atom would make things different from not > including > > it in this case, either. Any help would be appreciated. > > > > Mala > > > > On Tue, Feb 5, 2019 at 11:37 AM Mala L Radhakrishnan < > > mradh...@wellesley.edu> > > wrote: > > > > > Hi, > > > > > > I am trying to extract snapshots and center on a particular group, but > > the > > > center of the box does not correspond to the geometric center of the > > group > > > as expected. It is centered on the outer edge of the group. Here is > the > > > command I am using: > > > > > > gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tpr -b 201000 -e 201000 > -n > > > INDEX.ndx -center > > > > > > ...and I then choose the group in the index file that corresponds to > what > > > I want right in the center; I have verified the correctness of the > index > > > file. I ran my simulation with pbc but in this case I specifically > want > > to > > > maintain the same cubic box used in the simulations, so I don't want to > > > keep molecules whole. So all I want to do is extract the cubic box > that > > is > > > centered on the group I want. But the resulting snapshot has the > > molecule > > > slightly (about 10%) off center, mainly in the y direction in this > > case. I > > > presume that center will place the geometric center of the group you > > choose > > > at the geometric center of the box. Am I incorrect? Is there another > > way > > > to accomplish what I want? > > > > > > Thank you so much, > > > > > > Mala > > > > > > > > > -- > > > Mala L. Radhakrishnan > > > Whitehead Associate Professor of Critical Thought > > > Associate Professor of Chemistry > > > Wellesley College > > > 106 Central Street > > > Wellesley, MA 02481 > > > (781)283-2981 > > > > > > > > > -- > > Mala L. Radhakrishnan > > Whitehead Associate Professor of Critical Thought > > Associate Professor of Chemistry > > Wellesley College > > 106 Central Street > > Wellesley, MA 02481 > > (781)283-2981 > > -- > > 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. > > > > > -- > --------------------------- > Gyorgy Hantal, PhD > Postdoctoral Fellow > Dept. of Computational Physics, University of Vienna > Sensengasse 8/9, 1090 Wien, Austria > gyorgy.han...@univie.ac.at <gyorgy.han...@gmail.com> > Tel. +43-(0)1-4277-73292 > -- > 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. > -- Mala L. Radhakrishnan Whitehead Associate Professor of Critical Thought Associate Professor of Chemistry Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- 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.
