[gmx-users] extended calculation pdb extracttion query
Deep kumar
deepak.choubey86 at gmail.com
Wed Sep 20 14:40:01 CEST 2017
Hi 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.
Thanks,
DK
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