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

XAvier Periole x.periole at rug.nl
Thu Jun 10 17:04:23 CEST 2010

On Jun 10, 2010, at 4:54 PM, 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
If this command does not work that means your tpr file (reference
structure) contains broken subunits. Check it and give a tpr with the
subunits full and it will work ...

> 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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