Re: [AMBER] RMSD analysis

From: Daniel Roe <>
Date: Fri, 8 Jan 2021 16:09:54 -0500


One thing to watch out for are imaging artifacts, which can make the
RMSD seem to suddenly spike. Some typical cpptraj input would be
something like this:

parm myparm.parm7
# Remove water if present
strip :WAT
# Reimage
# Calculate RMSD to first frame for alpha carbons
rmsd CaToFirst .CA first out

The '.agr' extension will format the data file for XMGRACE - use
'.dat' for a "regular" data file.

Hope this helps,


On Thu, Jan 7, 2021 at 5:35 PM K Jan <> wrote:
> Hi Amber users,
> I`m trying to calculate the RMSD of a 90 ps simulation of a molecule with
> cpptraj.
> The rmsd increases from 0 to 17 Angstroms in the 90 ps which is clearly too
> big. I`ve also checked the vmd and my molecule is translating around the
> screen a small amount and vibrating a little, but the structure of it
> doesn't change at all, which is strange because the radius of gyration has
> increased, which should mean that the compactness of my molecule has
> decreased but that hasn`t happened.
> I read that I have to perform a least-squares fit to remove the global
> rotation and translation. I am not sure how to do this and would appreciate
> some advice. I read that I could do this on the vmd by using the rmsd
> trajectory tool but when I try and press align in the tool it says that no
> atoms have been selected, even though I wrote protein in the atom selection
> box, and I have loaded up the topology of my molecule and the trajectory
> files from my simulation.
> Would appreciate some help.
> Thanks ,
> Kris
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Received on Fri Jan 08 2021 - 13:30:02 PST
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