demux(1)

💖 demux(1) — the GROMACS suite's lil trajectory-unscrambler 💖

okay so bestie, this is demux, from the General Commands Manual section of the GROMACS suite, and she is here to save your REMD trajectories from being a chaotic mess. let's get into it 🫶

✨ NAME ✨

demux — Convert XPLOR distance restraints to Gromacs format

(yes girl, that's what it says. we keep it exactly as written. iykyk 💅)

🌸 SYNOPSIS 🌸

demux md0.log extra

🦋 DESCRIPTION 🦋

so. if you would like to make your trajectories continuous again (and honestly? who wouldn't), you can use demux to read your md0.log file — and yes, you can concatenate several of them if you need to — and she will produce a few output files for you. periodt.

one of these is a .xvg file, called replica_ndx.xvg, and you can pass that to trjcat(1) along with the original trajectory files, in order to produce continuous trajectories. slay. 🔥

the other file, replica_temp.xvg, contains the temperatures for each replica, starting at the original temperature. so if your replica of interest starts at, say, 300 K, you can follow its trajectory through temperature space. iconic.

it would be interesting to add some functionality to make histograms of temperature distributions for each replica, which according to most authors should be flat. (not us editorializing, that's literally what the page says 💀)

the demuxed trajectories can be used with g_kinetics(1) to obtain protein folding kinetics from REMD trajectories. main character energy honestly 👑

💅 OPTIONS 💅

• md0.log — Log file of the trajectory run you wish to make continuous. Multiple files can be appended together. yes bestie, stack 'em up 🎀
• extra — Number of times each entry in the log file will be copied. It's an integer, no decimals no vibes.

😭 LIMITATIONS 😭

okay this is the part where we get real. if your exchange was every N ps and you saved every M ps, you can make up for the missing frames by setting extra to (N/M - 1).

but if N/M is not an integer? you're out of luck, and you will not be able to demux your trajectories at all. 💀

fr fr. it's not giving flexibility, it's giving all-or-nothing. do the math before you commit, bestie.

🌈 SEE ALSO 🌈

• gromacs(7)
• trjcat(1)
• g_kinetics(1)
• <http://wiki.gromacs.org/index.php/REMD>

and that's the whole page, no cap ✨ this little queen comes to you from the GROMACS suite, Version 4.0, dated 13 Oct 2008 — old money, still serving 🎀💜 go demux those trajectories, you got this 🫶