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.
