Using NAMD trajectories?

[winsvern]

I have some trajectories produced using NAMD. I have tried to convert these to a form that will work in CHAP and failed. Is there a way to convert these trajectories to a format that is readable by CHAP?

Thank you in advance.

Vern Winston

[Inniag]

I've never worked with NAMD, but I have successfully converted *.dcd trajectories produced by OpenMM to Gromacs' *.xtc format using the MDAnalysis library. The converted trajectory can then be used as input for the -f flag of CHAP. A corresponding PDB file can be used for the -s flag.

A conversion script might look like this:

import MDAnalysis as mda

# load NAMD trajectory, PDB file is needed to define topology
u = mda.Universe("structure.pdb", "trajectory.dcd")

# select all particles
system = u.select_atoms("all")

# write to XTC trajectory
with mda.Writer("converted_trajectory.xtc", system.n_atoms) as w:
    for ts in u.trajectory:
        w.write(system)

Hope this helps!

[winsvern]

The script works perfectly (after I got openMM and MDanalysis up and running). The converted trajectory and pdb file are accepted by CHAP. Progress. Now I have to fix some problems with my NAMD run, and will be on my way. (Eventually I want to convert this project to GROMACS, and that would make everything easier, but that is for another day)

Thank you again. You saved me a huge amount of time.

Vern Winston

On Thu, Jan 23, 2020 at 7:01 AM Inniag notifications@github.com wrote:

I've never worked with NAMD, but I have successfully converted .dcd trajectories produced by OpenMM to Gromacs' .xtc format using the MDAnalysis https://www.mdanalysis.org/ library. The converted trajectory can then be used as input for the -f flag of CHAP. A corresponding PDB file can be used for the -s flag.

A conversion script might look like this:

import MDAnalysis as mda

load NAMD trajectory, PDB file is needed to define topology

u = mda.Universe("structure.pdb", "trajectory.dcd")

select all particles

system = u.select_atoms("all")

write to XTC trajectorywith mda.Writer("converted_trajectory.xtc", system.n_atoms) as w:

for ts in u.trajectory:
    w.write(system)

Hope this helps!

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[Inniag]

Glad I could help! I hope CHAP proves useful for your project. Good luck with your NAMD to Gromacs migration.