Hi

Angana Ray,

Is there a way to treat the trajectories using gromacs? If yes, I think I can help you:

- Create a index for the protein and the nucleic acids;

- Using the gmx trjconv command, add the following flags: -pbc mol -ur compact -center;

- If you want to jump all the solvent outside the box (not that cool visually), use then: -pbc nojump -center.

Gromacs will ask you the first index for centering, so select the index you have created for the protein | nucleic acids. Further, in the output option you can select the system (or only the complex, if you want).

I hope it helps.

Best.

I cannot use gmx because I have my files in desmond format !!

Hello Angana Ray, the "unwrap" command should work in VMD. You can try the following steps:

1. Save one of the trajectory frames as PDB.

2. Load the PDB and go to Graphics > Representation.

3. Try to visualize only the molecule(s) of interest using specific "atomselect" keywords.

https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node79.html#table:ug:keywords

4. If the visualization works, then use that selection with the "unwrap" command.

pbc unwrap -sel "