Hello all.
I need to calculate the average structure of a protein from a 100ns trajectory. I came across two commands - gmx cluster and gmx covar. I tried gmx clusters, but the structure I got at the end of the run is physically not correct. When I tried gmx covar it does provide an average structure, but the problem it starts Diagonalizing the covariance matrix, which is very costly. Can anyone suggest me how to deal with this problem ?
How does this average structure calculation work for these two commands ?
Can I stop running the gmx covar command after getting the average structure without the Diagonalizing part ?
Thank you so much.