[gmx-users] Removing periodic boundary condition

[Sanket Ghawali]

Dear, gmx-users,

Hello everyone,
I'm simulating a peptide in an SDS micelle. The simulation was
performed for 100ns
When I view the trajectory in VMD, a portion of the SDS micelle moves
to the right and goes into the next box. Of course, because of
periodic boundary conditions. I tried using trjconv to see if I could
suppress the periodic boundary conditions for the purpose of
visualization. I've used all the different -pbc options none of them
helped.

options i have used

trjconv -f .trr -s .tpr -o nojump.trr -pbc nojump

used the above created nojump.trr in the below command

trjconv -f nojump.trr -s .tpr -n .ndx -o .trr -b 0 -e 100000 -ur
compact -pbc mol -center

Selected Protein&sds as centering group and system as output group


Any suggestions on how to go about doing this?

Thanks,

Sanket