Re: Question about PBC and RMSD

From: Pratik Narain Srivastava (
Date: Sat Oct 10 2020 - 03:22:28 CDT

Why do you need to simulate the 3 chains? In many PDB entries, multiple
chains exist as a part of the result of X ray crystallization which doesn't
completely reflect the biological nature of that protein. If you provide
the pdb id of your interest, I might help you better.

On Sat, Oct 10, 2020, 11:03 AM alli suliat <> wrote:

> 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
> this?
> Thank you in advance
> Sincerely,
> Adeola Alli

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