Hi all
I've a challenge with how to remove pbc conditions accurately
my simulation results contain a few micelle clusters including polymers. I have to do some msd analysis afterwards. So I need to get a continuous trajectory by removing pbc conditions using gmx trjconv tool first. I tried different sequence of steps that I thought might solve the problem, but none worked. I included a few here:
1- try 1 (steps): a) use gmx trjconv -pbc cluster, to find the clusters. problem: clusters move from one side to another in different frames.
2- try 2 (steps): following micelle clustering of manual.gromacs.org/documentation/2019.4/how-to/visualize.html a) make a new tpr file using a structure in a frame that micelles are formed. b) use gmx trjconv -pbc nojump problem: structure of molecules at same frames are different from the main trajectory, polymers are separated from.
3- others: I used multiple combinations of -pbc -fit to remove the pbc effects, none solved the problem and still micelles are loosing molecules compared to main trajectory.
I've been struggling with this issue for a few days, I highly appreciate if you could help me about this issue. Please let me know if I need to provide further
Thank you very much
Arash Elahi You can refer to the suggested workflow described here: http://www.gromacs.org/Documentation_of_outdated_versions/Terminology/Periodic_Boundary_Conditions
I could not get exactly which is your problem. But I infere that you want that all the molecules are inside the box, without jumping??
If it is what you want, you need to center your trajectory (all the frames I mean), on what you think that the center of your system is (for this you need to use the flag -center when you use gmx trjconv, the first group that you would choose would be use to center your system in the whole trajectory, and the second one is for which part of the system would you want to save), and the flag -pbc mol, so your molecules (or everything that was defined as a molecule) would be all together.
Hope I am be clear enough.
Cheers
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