I have been processing some trajectory files from my molecular dynamics simulation using GROMACS by removing pbc, which often requires a sequence of gmx trjconv steps. This time, my protein appears split into pieces, and after applying -pbc whole there is still a clear split causing errors in RMSD calculations. Even further, if I apply cluster or nojump there is a clear also a split down the center of the molecule. Are there other ways to correct pbc aside from gmx trjconv with whole, nojump, cluster, center, or fit? If anyone has experienced this or has a suggestion on how to resolve this, I would greatly appreciate it. Thank you.
Kaitlyn Swayze attached link for GROMACS User Manual 4.6.3:
https://idoc.pub/documents/gromacs-manual-klzz22m89vlg
Employing tpbconv, supply the old checkpoint file directly to mdrun with -cpi.
Good luck.
Have a look at https://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html and https://www.biorxiv.org/content/10.1101/2020.04.25.060269v1.full.pdf
Kaitlyn Swayze attached link for GROMACS User Manual 4.6.3:
https://idoc.pub/documents/gromacs-manual-klzz22m89vlg
Employing tpbconv, supply the old checkpoint file directly to mdrun with -cpi.
Good luck.
Pradeep Paraman and Muhammad Ali
Thank you for your reply and guidance. I notice that in the 2020.2 version tpbconv is now convert-tpr (noted here: https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html?highlight=tpbconv). With this, I am slightly confused as to the goal. Is the objective to create a new tpr file and begin the simulation from the point where this error occurs? And in this case, is the input to convert-tpr the previous tpr file and just use -extend? So far, I have been using convert-tpr to extend the simulation, and supplying the prior checkpoint file to mdrun. My protein is also trimeric, and I am not sure if this has an impact on the potential solution.
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