As far as I understand, the H5MD file doesn’t have any information on boundary conditions. It just has the box dimensions. I don’t know what could be the issue. Please let me know if I can test something else.
Thanks, Aditi. On Wed, Mar 27, 2019 at 7:05 PM Christoph Junghans <jungh...@votca.org> wrote: > > > On Wed, Mar 27, 2019, 17:15 Aditi Khot <khota...@gmail.com> wrote: > >> This is the output: >> >> Boundary Condition: orthorhombic >> >> Box matix: 27ybe .3069 0 0 >> >> 0 27.3069 0 >> 0 0 27.3069 >> > > Ok, so actually get read as expected here! > So the topology reader works. > Maybe the h5 trajectory has open boundary conditions saved in it. > > The trajectory can overwrite the box size and boundary conduction to allow > for changing box sizes, e.g. in npt simulations. > > Jakub, do you have an idea? > > Christoph > > Thanks, >> Aditi. >> > >> On Wed, Mar 27, 2019 at 4:55 PM Christoph Junghans <jungh...@votca.org> >> wrote: >> >>> >>> >>> On Wed, Mar 27, 2019, 14:33 Aditi Khot <khota...@gmail.com> wrote: >>> >>>> I did that using '<box xx="27.3069109148" yy="27.3069109148" zz= >>>> "27.3069109148" />' >>>> But it still gives this warning 'NOTE: You are using OpenBox boundary >>>> conditions. Check if this is intended.' >>>> >>> I see, can you run your xml file through csg_dump --top and see if the >>> box size is reported correctly? >>> >>> Christoph >>> >>> >>>> Thanks, >>>> Aditi. >>>> >>>> On Wednesday, March 27, 2019 at 3:07:45 PM UTC-4, Christoph Junghans >>>> wrote: >>>>> >>>>> >>>>> >>>>> On Wed, Mar 27, 2019 at 13:53 Aditi Khot <khot...@gmail.com> wrote: >>>>> >>>>>> Hi Christoph, >>>>>> >>>>>> Thanks for the reply. I had another question. If I am have an >>>>>> atomistic trajectory file with periodic boundary conditions, do I need to >>>>>> unwrap the coordinates before supplying it to VOTCA? I could not find an >>>>>> option to specify boundary conditions. >>>>>> >>>>> There is an option in the xml topology to set the box size. If you do >>>>> that periodical boundaries are assumed and minimum image convention is >>>>> applied. Otherwise open boundaries are used. >>>>> >>>>> Christoph >>>>> >>>>>> >>>>>> >>>>>> Thanks, >>>>>> Aditi. >>>>>> >>>>>> On Tuesday, March 26, 2019 at 8:15:11 PM UTC-4, Christoph Junghans >>>>>> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Mar 26, 2019, 17:49 Aditi Khot <khot...@gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I want to perform force matching using VOTCA. My group uses LAMMPS >>>>>>>> for MD simulations. So, I am generating a '.h5' file to supply as a >>>>>>>> trajectory file to VOTCA. I do not have '.tpr' file for topology, so I >>>>>>>> am >>>>>>>> defining the atomistic topology in an xml file according to Pg. 14 in >>>>>>>> VOTCA >>>>>>>> manual. >>>>>>>> >>>>>>>> I wanted to reconfirm if this will work. And should I supply the >>>>>>>> topology xml file as argument to '--top' option? Please clarify these >>>>>>>> doubts. >>>>>>>> >>>>>>> Yes, that should be fine, you can combine pretty much all topology >>>>>>> files with all trajectory files. >>>>>>> >>>>>>> Christoph >>>>>>> >>>>>>>> >>>>>>>> Thanks in advance! >>>>>>>> >>>>>>>> Aditi. >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> You received this message because you are subscribed to the Google >>>>>>>> Groups "votca" group. >>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>> send an email to votca+un...@googlegroups.com. >>>>>>>> To post to this group, send email to vo...@googlegroups.com. >>>>>>> >>>>>>> >>>>>>>> Visit this group at https://groups.google.com/group/votca. >>>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>>> >>>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "votca" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to vo...@googlegroups.com. >>>>>> To post to this group, send email to vo...@googlegroups.com. >>>>>> Visit this group at https://groups.google.com/group/votca. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> -- >>>>> Christoph Junghans >>>>> Web: http://www.compphys.de >>>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to votca+unsubscr...@googlegroups.com. >>>> To post to this group, send email to votca@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/votca. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to votca+unsubscr...@googlegroups.com. >>> To post to this group, send email to votca@googlegroups.com. >>> Visit this group at https://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >> -- >> Aditi Khot, >> Dual Degree Final Year, >> Chemical Engineering, >> Indian Institute of Technology, Madras. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to votca+unsubscr...@googlegroups.com. >> To post to this group, send email to votca@googlegroups.com. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- Aditi Khot, Dual Degree Final Year, Chemical Engineering, Indian Institute of Technology, Madras. -- You received this message because you are subscribed to the Google Groups "votca" group. 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