[gmx-users] Syntax to use "gmx convert-tpr"

[Zhang, Cheng]

Dear GROMACS experts,

Can I ask if the following commandlines are correct for extending simulations?


gerun convert-tpr -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md_0_1.tpr

gerun mdrun_mpi -deffnm md_0_1 -cpi md_0_1.cpt -maxh 0.5 -append


(My job.sh can be found at https://copy.com/lrFubrlq9fos04Zy)


My questions are:


1) For the 1st job, there are no .trr and .edr files. So the "convert-tpr" will be ignored?


2) Should I use "-f md_0_1.trr" or "-f md_0_1.cpt" as shown on

http://manual.gromacs.org/programs/gmxconverttpr.html   ?


3) What is "index.ndx" file used for? I cannot find them as outputs of a simulation. Do I need to include that?


Thank you very much.


Yours sincerely

Cheng