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.
