Hi, There are a few issues related to gmx trjconv -center:
a) http://redmine.gromacs.org/projects/redmine-platform/search?all_words=1&attachments=0&commit=Submit&issues=1&options=0&page=1&q=-center&scope=all&titles_only=&utf8=%E2%9C%93 b) http://redmine.gromacs.org/issues/2579 but not sure if the exactly match what you have. Benson On 2/6/19 7:39 PM, Mala L Radhakrishnan wrote: > ...and as a follow up, it doesn't seem to be centering at either the > geometric center OR the center of mass. Any insight would be appreciated. > > Mala > > On Wed, Feb 6, 2019 at 10:15 AM Mala L Radhakrishnan <mradh...@wellesley.edu> > wrote: > >> 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.
