replica_exchange(1)

📦
version 9.9 · 3 versions
, in debian bookworm, ubuntu jammy, ubuntu noble

💖 replica_exchange — the manual, but make it make sense 💖

okay bestie, sit down, hydrate, because we're about to talk about replica_exchange from the Cooperative Computing Tools, manual section 1. this one is a whole moment. 🫶

✨ NAME ✨

replica_exchange — a Work Queue application for running replica exchange simulations using ProtoMol. yes, that's the whole name. short. iconic. she knows what she is. 💅

🌸 SYNOPSIS 🌸

replica_exchange [options] <pdb_file> <psf_file> <par_file> <min_temp>
<max_temp> <num_replicas>

🦋 DESCRIPTION 🦋

so, replica_exchange is a Work Queue application for running replica exchange simulations using the ProtoMol simulation package. and listen — she supports both barrier and non-barrier based runs. versatile queen. 👑

the barrier based run transfers the configuration files and input data for each replica to the connected work_queue_worker() instances, runs the ProtoMol simulation package, and gathers the output, at every single Monte Carlo step. it literally waits for the simulation of all replicas to finish at each step before it moves on to the next step, which means yeah, it incorporates a barrier at every step. no skipping ahead, no cutting corners. and at the end of every step? it randomly picks two neigboring replicas, applies the metropolis criterion, and if that criterion is satisfied, it swaps the parameters of the two replicas and keeps the simulations going. 🎀

the non-barrier based run is equivalent to the barrier run in the output and results it produces. same vibes, same receipts. BUT it avoids using a barrier by running multiple monte carlo steps for each replica until that replica gets picked to attempt an exchange. by default, the application will run using this non-barrier implementation. so that's the default girlie. ✨

the pdb_file, psf_file, and par_file arguments specify the input files required for the simulation run. the min_temp and max_temp specify the temperature range in which the replicas are simulated. and the number of replicas being simulated is given by num_replicas. that's the whole roster. 💜

replica_exchange can be run on any machine accesible to work_queue_worker instances. anywhere. she travels. 🌈

🎀 OPTIONS 🎀

  • -n <name> — Specify a project name for using exclusive work_queue_worker instances. it's giving ✨exclusive✨.
  • -x <filename> — Specify the name of the xyz file for output.
  • -d <filename> — Specify the name of the dcd file for output.
  • -m <number> — Specify the number of monte carlo steps. Default = 100.
  • -s <number> — Specify the number of molecular dynamics steps. Default = 10000.
  • -p <path> — Specify path for storing output files.
  • -q — Assign closer temperature values to replicas in the first and last quartile.
  • -i — Assume ProtoMol is installed and available in PATH on worker site.
  • -b — Use barrier in waiting for all replicas to finish their steps before attempting exchange.
  • -l — Print debuggging information. (yes, that's spelled exactly like that in the original, and no, i'm not touching it. leaving it alone out of respect. 💀)
  • -h — Show this help message.

💀 EXIT STATUS 💀

On success, returns zero. On failure, returns non-zero. that's it. that's the tea. 🍓

🧚 ENVIRONMENT VARIABLES 🧚

if the cctools are installed in a non-system directory, such as your home directory, then you must set the PYTHONPATH environment so that the workqueue python module can be found. for example:

% setenv PYTHONPATH $HOME/cctools/lib/python2.4/site-packages
don't skip this bestie, she will NOT find her module and you will be sad. 😭

🔥 EXAMPLES 🔥

to run a replica exchange experiment with 84 replicas in the temperature range 278 to 400K using the sample input files:

% replica_exchange ww_exteq_nowater1.pdb ww_exteq_nowater1.psf par_all27_prot_lipid.inp 278 400 84

to run a replica exchange experiment, with project name ReplExch, over 250 Monte Carlo steps running 1000 molecular dynamics steps and involving 84 replicas in the temperature range 278 to 400K using the sample input files:

% replica_exchange -N ReplExch -m 250 -s 1000 ww_exteq_nowater1.pdb ww_exteq_nowater1.psf par_all27_prot_lipid.inp 278 400 84
👀 yes, the second example uses -N while the option list says -n. that's just how it is in the original, so i'm keeping it exactly as-is. no notes. 🙈

The Cooperative Computing Tools are Copyright (C) 2005-2019 The University of Notre Dame. This software is distributed under the GNU General Public License. See the file COPYING for details.

🌟 SEE ALSO 🌟

and that's the whole page, bestie! 💖 this edition is from CCTools 8.0.0 DEVELOPMENT — that's the version stamped on the page, dated right there on the original footer alongside replica_exchange(1). slay, go run some simulations, and remember: no cap, the facts stay exactly the same even when the vibe is immaculate. periodt. ✨💅🦋

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