Hi, I'm using Gromacs 4.5.5 to simulate a protein in explicit solvent. The simulation is running fine and I have collected 9 100ns simulations. I'm eliminating the first 50 ns for equilibration and sheer data size. What I want to do now is to cluster the simulations based on rmsd of certain residues. I have used make_ndx to select the residues and made a group. I have used trjcat -cat option to concatenate the 9 runs into a single giant .xtc file. In the .xtc file, I only output the protein. My plan was to use g_rms to create a rmsd.xpm table and using that with g_cluster. However, when I do run g_rms, it seems like it will take weeks to finish. The RMSD matrix size becomes 225000x225000 and my question is: How do you cluster this much data? Any recommendation would be useful.
Thank you for your time.
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