Fellow Gromacs users: Suppose I run a 1 ns equilibration on my protein system prior to molecular dynamics, and I am converting the equilibration trajectory to a TPR file. Correct me if I'm wrong here - I'd like to confirm that I can generate a TPR file by using frames accessed in the ENTIRE trajectory, or just certain frame(s), i.e. last snapshot.
1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md.gro 2. grompp -f md.mdp -c protein_b4md.gro -p topol.top -o protein_md.tpr 3. editconf -f protein_md.tpr -n index.ndx -o protein_md.pdb As compared to using the very last frame in the equilibrated trajectory: 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md_1ns.gro -b 1000 -e 1000 2. grompp -f md.mdp -c protein_b4md_1ns.gro -p topol.top -o protein_md_1ns.tpr 3. editconf -f protein_md_1ns.tpr -n index.ndx -o protein_md_1ns.pdb Does the former method output a structure that is an "ensemble average" based off of the equilibration time? If it is indeed an average, should I use RMSD clustering to extract an actual structure accessed in the trajectory that is closest to the ensemble average? Any suggestions would be greatly appreciated here. Sincerely, Lily -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
