[gmx-users] Fwd: extended calculation pdb extracttion query

Deep kumar deepak.choubey86 at gmail.com
Thu Sep 21 14:24:30 CEST 2017

Dear ALL,

I have run an extended simulation for 90ns like this: (my previous run was
for 10ns)

grompp -f new.mdp -c old.tpr -o new.tpr
mdrun -s new.tpr -cpi old.cpt

because, I had to make changes in the .mdp file. I have got new files
from the new extended run;

new.tpr, new.xtc  ....etc

My 10ns mdrun results are like old.tpr, old.xtc   ...etc

Now, I want to get the pdb files from the runs (10ns + 90ns). Can you
please let me know how can I do it? I know to get the pdb files from mdrun
I should do this:

gmx trjconv -s new.tpr -f new.xtc -dt 100 -o trj.pdb

but I want to combine both 10ns and 90ns and get the pdb files.


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