[gmx-users] Removing periodic boundary condition

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 16 10:10:27 CEST 2016

Hi Sanket,

Can you check the structure in the tpr file (editconf -f .tpr -o
.gro/.pdb)? If that is good, then -pbc nojump should work. For the second
pass, you shouldn't need -pbc mol then.


On May 16, 2016 9:06 AM, "Sanket Ghawali" <sanket.ghawali at gmail.com> wrote:

> 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
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