[gmx-users] problems when using command "trjconv"

[mircial at sjtu.edu.cn]

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