Hi Peter,
Thank you so much for your fast reply. Changing from MDAnalysis to MDTraj for centering the Trajectory was the best idea and solved my issue.
I should have done it earlier.
Search found 2 matches
- Wed Jan 10, 2024 8:31 am
- Forum: OpenMM
- Topic: Saving Topology after OpenMM simulation
- Replies: 3
- Views: 832
- Tue Jan 02, 2024 9:51 am
- Forum: OpenMM
- Topic: Saving Topology after OpenMM simulation
- Replies: 3
- Views: 832
Saving Topology after OpenMM simulation
Hi everyone, I love OpenMM but I am struggeling with one issue. I hope to get some input here: I am using MDAnalysis to analyze my trajectories. I have noticed that if I prepare everything with amber and run OpenMM from the prmtop and crd file, I am able to center my protein in the center of the wat...