[gmx-users] Regarding PBC

Dilip H N cy16f01.dilip at nitk.edu.in
Sun Apr 2 21:39:02 CEST 2017


I ran a energy minimization followed by nvt, npt, md simulation...and
during analysis, if i look my .gro file  structure in vmd and i write in
tkconsole as pbc box and see that *some  of the molecules are not inside
the box, they have been outside the box*, is there anything wrong..?? how
can i knw about this..?? any  influence of PBC....etc.,

how can i clear all these doubts..?? is there any prescribed
book/references for it...thn it would help a lot...

With Best Regards,

Ph.D Student

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