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

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 10 16:56:54 CEST 2010

mircial at sjtu.edu.cn 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).


> Best Wishes
> R-X Gu


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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