[gmx-users] using rerun to extract energies for protein fromtrr file

[Mark Abraham]

Siavoush Dastmalchi wrote:
> Dear Mark,
>  
> Many thanks for your kind suggestion. I did all sorts of things as you suggested, however still I get the same error. Here are the commands that I use (I used grompp also to generate different tpr files):
>  
> $ tpbconv -s fullmd.tpr -n index.ndx -o tpxout.tpr
> $ trjconv -f md_traj.trr -n index.ndx -s tpxout.tpr -o trajout.trr
> $ mdrun_d -s tpxout.tpr -o md_prot_final.trr -c md_prot_final.gro -e md_prot.edr -g md_prot.log -rerun trajout.trr
>  
> I am a bit confused and don't know what I am doing wrong. Is there any way to extract coordinates of just protein molecule for different frames and then calculate their energies (this is just a guess)?

Select just the protein group from the index file when using the *conv 
utilities? (I haven't actually ever done this procedure, but that's 
about how it should work)

Mark