Starting pdb file for trajectory analysis (gromacs MD)

[sayman]

Hi,

My trajectory file is originally from gromacs. I converted my final MD .xtc file to .dcd file using mdtraj. My question is: which is the appropriate starting pdb file to use for trajectory analysis in bio3d? My original pdb file (used in gromacs) has all its waters removed (as per standard gromacs md run). The system is then solvated, ions added and equilibrated (NVT and NPT ensembles). My guess is to use the resultant gromacs "_solv_ions.gro" file and convert it to pdb. Both my original pdb and solv_ions.gro work but give different results. Maybe even the md_0.1.tpr file (which contains run parameters, so probably not?). I've scoured your resources to find the answer but alas.

This forum is great. Thanks so much.

[Xinqiu Yao]

Hi,

You should use the pdb file containing exactly the same number of atoms as in the .dcd. You can check these numbers by reading both the .dcd and the .pdb files in R with bio3d. Let me know if you have any problem to do it.

[sayman]

So simple. Thanks for taking the time to help with such trivial questions.