I want to calculate the MMPBSA. i did MD simulation through Gromacs at 10ns. when i was calculting MMPBSA for 10ns its take a lot of time to finish. then i read some paper they mention that they did calcultion for 20snapshoots.
I want to do MMPBSA calcu;ltion for 50/100 snaphots from total snapshot.
please let me know how to extract the 50/100 snapshots from total snapshots for calculation of MMPBSA in less time.
Krishnendu Bera
Use gmx trjconv to extract the frames. You can use -dump or -sep flag.
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Vikram Dalal
you can use this following command to keep the trajectory from 8 ns to 10 ns:-
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o new_md_0_1.xtc -b 8000 -e 1000
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