GROMACS version: 2020
GROMACS modification: NO
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AFter successfully completing the simulations, we are trying to extract a single pdb frame from .xtc file.
For this we do recentering. The following are the commands:
- recentering command: gmx_mpi trjconv -s md_40ns.tpr -f md_40ns.xtc -o md_40ns_center.xtc -center -pbc mol -ur compact < ./recent.txt
- gmx_mpi trjconv -s md_40ns.tpr -f md_40ns_center.xtc -o 4PPF_2BA_outcomp3_40ns.pdb -dump 40 <./dump.txt`
After doing this, some times the ligand in the complex is found fragmented, some times it is fine with intact connectivity.
What could be the reason? Any interpretation w.r.t the unfavorable binding in the binding site?
During one simulation - fragmeted ligand appears. Same complex when repeated for simulation with same commands, the ligand is intact.
Please help explain the rational behind this behavior while using gromacs.
Thanks in advance,