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.'
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] <javascript:>> > 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
