Question about PBC and RMSD

From: alli suliat (
Date: Sat Oct 10 2020 - 00:31:11 CDT

Dear NAMD Experts,

I am a new user of the NAMD software. I'm using it to simulate a
protein-ligand complex. The protein has 3 chains. I used periodic
boundary conditions in the NAMD run of 40 ns. After simulating for about
20ns, I noticed one of the chains leaves the water box and returns. And
when I calculate the RMSD of the protein, I notice a huge increase in RMSD
around the time one of the chains left the box.
I have tried to use the PBC wrap command to recenter the protein and saved
as a new trajectory, but the issue still persists. Please, how do I resolve
Thank you in advance

Adeola Alli

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