Question: I have run a REMD simulation for a dimer and I concatenated the trajectory of all. This dimer during the simulation got separated in the middle to individual monomers and again forms dimer.
Now, I want to extract the trajectory removing pbc and use it for further analysis and also visualize the trajectory in the box.
But when I extract using no jump the trajectory file visualized in pymol shows many zig-zag lines.
And when I use other methods in gmx trjconv for extraction the dimer protein molecule shows one of its chain on one side of the box and the other chain on the other opposite end of the box which have same structure and mean that they are in contact and not separated.
So, I want a method for trajectory extraction of dimer where we can see the dimer as a whole if its not separated and see the dimer as two different chains if it got separated in the simulation at some point of time.
I have used a dodecahedron box.
Thank you @jalemkul , I think I got the dimer protein in a box without dissociation. But without doing the trajectory extraction using gmx trjconv -center -pbc mol -ur compact is there way to know whether they dissociate at any point of time in trajectory through any analysis process, so that I can confirm that my extraction is correct.
I tried using this command but it seems like it makes both the chains forcibly at center in some frames. And for all the frames both the chains remain at center. I am not sure if i can go on with this xtc file for further analysis.
I tried using gmx_mpi trjconv -f tra.xtc -s equil1/md.tpr -pbc whole -o final_traj.xtc -center
and I could see some frames having detached chains.
So, I am totally confused now whether the detached chains which I see are really dissociated or are periodic images which seem to be detached but aren’t.
Take a look at the post I made a while ago at the 3rd party tools section of this forum. mdvwhole will solve your problem and you do not need to fiddle with your trajectory. I do on know how you solvent is named, but after installing (takes a while as I did not clean the dependencies yet…) you should run the following command replacing WATER and IONS with their respective residue names in your system:
@jalemkul I tried to do RMSD and clustering both on the original (without removing pbc ) trajectory and on the no-pbc trajectory which I extracted using the command gmx trjconv -f tra.xtc -s equil1/md.tpr -pbc whole -o final_traj.xtc -center , but to my surprise I found both showing exactly the same results for number of clusters and cluster structures (clusters.pdb) and also the RMSD graph was exactly same. I did the RMSD using the chain A for least square fitting and Chain B for RMSD , and I used the rmsd.xpm file obtained as an output in gmx rms in gmx cluster -dm command as an input so that clustering can be done based on the rmsd (distance) between chain A and chain B (not considering the RMSD within each individual chains).
I don’t understand why it is giving the same result for PBC corrected and without PBC correction.
I used the above command for PBC correction (trajectory extraction) as the command suggested by you earlier gave results where the 2 chains in some frames seemed to be restricted to the center and thus all the frames had both chains at center as if there were still interactions.
And now I am not sure which extraction method is correct as one shows separation in some frames, the other shows no separation at all.
Some of the clusters also shows separation (procedure above) like below figure and I am not sure whether it is really a separation or not.