[gmx-users] Converting trajectory into tpr file

rainy908 rainy908 at yahoo.com
Tue Nov 6 01:25:31 CET 2012

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.


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