Jakub and Josh made a fix: https://github.com/votca/csg/pull/363 - please test it.
On Thu, Mar 28, 2019 at 8:19 AM Aditi Khot <[email protected]> wrote: > > 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. > 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.
