VMD-L Mailing List

From: Mcguire, Kelly (klmcguire_at_UCSD.EDU)
Date: Sun Mar 07 2021 - 14:31:30 CST

I was viewing the box around my periodic unit cell boundaries using PBCTools command: pbc box, and I see that it is shifted off my water box and protein system.

1) Does this mean my periodic boundaries are messed up?

2) I use the pbc box -shiftcenter {} command and get the pbc box centered on my water box and protein system again. However, the change does not save. How do I get my pbc box to stay/save centered on my waterbox/protein system?

I have a picture of the problem. If you want to see it, I can send it directly to you. Thanks!

Dr. Kelly McGuire
Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017