Dear All:
I encounter some problems when I am using command "trjconv" to remove
the periodic boundary condition.
I am doing molecular dynamics simulations of a pentamer, and some of
the subunits "jump" from one box to its adjacent one. Thus, I try to
remove the periodic boundary conditions by trjconv command.The
commands I used are as follows:
trjconv -s trpfile -f xtcfile -o new_xtcfile -n index.ndx -pbc nojump
In the results I found the five subunits are put together to form the
initial pentamer which is what I expected. However, I also found some
of the subunits are cut off a part (i.e., the subunit is broken into
one large piece and several small pieces, the large piece forms
pentamer with other subunits, and the small pieces distribute in the
boundary of the box).
Then, I try to solve this problem by using the follow command:
trjconv -s trpfile -f new_xtcfile_lastCommand -o another_new_xtcfile
-n index.ndx -pbc whole
this time, the subunits are not broken, but the pentamer is not
formed(i.e., some subunits in one box and some in the adjancent one).
Thus, I am writing to find a way in order to remove the periodic
boundary condition and put the subunits together as a pentamer with
out break a seperate subunit into several parts.Could anyone be so
kind to give me some suggestions? Thank you very much for your insight.
Best Wishes
R-X Gu
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