Dear Zhicheng, votca does not fix if molecules are broken along pbc. You can use gromacs to do that: trjconv -pbc mol ...
This is a sanity check, if your molecule is really bigger than half of the box AND you put the whole molecule into one bead, you m ight want to disable this check. Also see here: https://groups.google.com/forum/#!msg/votca/7qikLTcqu2M/coCq-zZYR9AJ This currently requires tweaking the code, if you really need it let me know. Best, Victor 2013/9/17 Zhicheng <[email protected]> > Hi: > > When I am mapping the polymer to coarse-grained bead, I get the > following error message:****** > > an error occurred: coarse-grained bead is bigger > than half the box **** > > ** ** > What is wrong with this? How can I fix it? I am very appreciating for > anyone's help. > > -- > 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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
