Okay. Thank you. I will do that. On Wed, Mar 27, 2019 at 11:16 PM Christoph Junghans <[email protected]> wrote:
> > > 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. > 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. 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