[email protected] wrote:
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.
Another option is to choose a residue near the central interface of the pentamer
and assign it to an index group, then use trjconv -center (choosing this residue
as the group to center).
-Justin
Best Wishes
R-X Gu
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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