Root mean square inner product (RMSIP) and PCA

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

I am new to gromacs and protein simulation. I have one modified protein and 1 one wild protein. i have performed PCA analysis on these 2 trajectories separately. and now want to calculate root mean square inner product.
pleas guide me if this is the correct way to perform PCA and how can I calculate RMSIP

2

You don’t specify the inner product of what and over what to take the mean.

gmx anaeig computes the inner product matrix of eigenvectors with -inpr and there are more overlap options. See the manual page:
https://manual.gromacs.org/current/onlinehelp/gmx-anaeig.html

3

sorry for not being clear. i want to calculate the inner product of 1st 10 PCs of the replicas for my each protein. i wan to establishes how conformational sub-space is captured by the first 10 PCs for each protein

4

You can use gmx anaeig -inpr and then manually sum up the terms.