Dear Gromcas users, I am quite new to Gromacs and I have just completed 100 ns simulation of a membrane protein using Gromcas. Now, I would like to do some basic analysis like RMSD, RMSF, Hydrogen bonding etc with the 100 ns trajectories. Below, I just wrote down the steps I adapted to generate the necessary preparatory files for different analysis with Gromacs analysis tools. I will be grateful if the experts in the community can help me with the their suggestion, if I am doing anything wrong here.
Step-1 : Concatenate all the trajectories, which I have run as 5 ns window each, and generate a single 100 ns trajectory. gmx trjcat -f 1md.trr 2md.trr 3md.trr 4md.trr 5md.trr 6md.trr 7md.trr 8md.trr 9md.trr 10md.trr -o 1_10md_concat.xtc Step-2: Remove the PBC gmx trjconv -f 1_10md_concat.xtc -o noPBC.xtc -s md.tpr -pbc mol -ur compact Step-3: Make the necessary index file if one want to do analysis with any specific group of atoms/molecule gmx make_ndx -f md.gro -o index.ndx Step-4: Do the analysis with different Gromcas analysis tools ( gmx rmsd, gmx cluster etc.) using the files from step-2 and step-3 Am I doing any thing wrong here? Is there any fine tuning required in these steps? Is there a way to combine the steps 1 and 2? Many thanks in advance Anu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.