On Wed, Mar 27, 2019, 20:05 Aditi Khot <[email protected]> wrote: > 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. > Jakub should know, he wrote the h5md reader for VOTCA. If you could do a minimal example to reproduce the problem and open an issue on GitHub with the input files attached that would be great.
Christoph > Thanks, > Aditi. > > On Wed, Mar 27, 2019 at 7:05 PM Christoph Junghans <[email protected]> > wrote: > >> >> >> On Wed, Mar 27, 2019, 17:15 Aditi Khot <[email protected]> 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 <[email protected]> >>> wrote: >>> >>>> >>>> >>>> On Wed, Mar 27, 2019, 14:33 Aditi Khot <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 [email protected]. >>>>>>>>> To post to this group, send email to [email protected]. >>>>>>>> >>>>>>>> >>>>>>>>> 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 [email protected]. >>>>>>> To post to this group, send email to [email protected]. >>>>>>> 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 [email protected]. >>>>> To post to this group, send email to [email protected]. >>>>> 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 [email protected]. >>>> To post to this group, send email to [email protected]. >>>> 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 [email protected]. >>> To post to this group, send email to [email protected]. >>> 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 [email protected]. >> To post to this group, send email to [email protected]. >> 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 [email protected]. > To post to this group, send email to [email protected]. > 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. 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