Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Bias-exchange metadynamics implementation #734

Draft
wants to merge 31 commits into
base: master
Choose a base branch
from
Draft

Bias-exchange metadynamics implementation #734

wants to merge 31 commits into from

Conversation

giacomofiorin
Copy link
Member

This PR contains an implementation of bias-exchange metadynamics (https://doi.org/10.1021/jp067873l) based on the NAMD Tcl scripting interface.

Although most of the code is Tcl, the following significant changes are introduced to the C++ source code:

  • The value of the "active" flag of the biases is being written to the state file; this is needed because all biases are defined for all replicas, but only one is active at a time. Therefore, we need to carry over the active flag when checkpointing.
  • The value of the "active" flag can be reported on the trajectory.
  • The field name is now a member of colvardeps, and could later be moved to the AST (see [RFC] Work towards reusable CVCs #700 (comment) and related comments).
  • Allow updating and reporting in the scripting calls the energy and forces of a bias, but without actually sending those (used to decide the exchanges).
  • Adds a neutral bias, which simplifies greatly the inclusion of replicas with equilibrium sampling in the BE implementation.

@giacomofiorin giacomofiorin added NAMD script_API Control Colvars from scripts labels Oct 18, 2024
giacomofiorin and others added 28 commits October 18, 2024 13:47
@giacomofiorin
Partial implementation of features restart (limited to active flag fo…
4b9c8e9 
…r now)

Started with the "active" flag, which is the most prominent example of a
feature that is not being set from the configuration file.
@giacomofiorin
Re-enable inactive colvars when writing a state
84fdd6a 
This prevents an error that would otherwise be raised due to the computed
value being inconsistent with the value from the state file (because the
latter was out of date when the state file was written).
@giacomofiorin
Initial implementation of Tcl bias-exchange scripts
a507562
@giacomofiorin
Store name of object in base class (colvardeps)
2199e8e
@giacomofiorin
Allow reporting feature states to trajectory
cefddfd 
Using this new feature to track the status of biases in BE-MTD
@giacomofiorin
Set BE frequency from command
621cb87
@giacomofiorin
Reactivate all variables (some may have been inactivated by dependency)
afeb9a4
@giacomofiorin
Simplify manual definition of biases
757ac34
@giacomofiorin
Create example folder and README
c2a516c
@giacomofiorin
Simplify input, add equilibrium run
b36b21a
@giacomofiorin
Re-enable thermostat
82b7afc
@giacomofiorin
Use narrower Gaussians, move upper wall closer
55252d5
@giacomofiorin
Add trajectory post-processing script & basic documentation
d17f710
@giacomofiorin
Some README updates, minor code tweaks
a5c2abd
@giacomofiorin
Specify implementation constraints
f324b21
@giacomofiorin
Add neutral bias to simplify bias-exchange protocol syntax
cb59904
@giacomofiorin
Amend bemtd example to include neutral bias
87d6235
@giacomofiorin
Small improvements
b74b6a3
@giacomofiorin
Update post-processing script to correctly handle "neutral" biases
efa6416
@giacomofiorin
Fix missing state I/O code for neutral bias
80a6b05
@giacomofiorin
Begin phasing out protocols where neutral replicas have no bias
fec8a83
@giacomofiorin
Some doc updates
e7cc6e6
@fabsugar @giacomofiorin
Modified load_trajectories.py script to write in output a unique traj…
f04dac3 
…ectory sorted by time

at constant bias, histograms are now optional
@giacomofiorin
Use more precise type in return code setter
fa28956
@giacomofiorin
Access bias energy and applied forces via scripting
77a051a
@giacomofiorin
Use calcenergy & calcforces to avoid evolving the bias during exchanges
74fecdd
@fabsugar @giacomofiorin
Added step to header when writing output traj through load_trajectori…
6d362bf 
…es.py
@giacomofiorin
Update formatting of feature state and ignore it in diffs
04585e6
@giacomofiorin giacomofiorin modified the milestones: NAMD 3.1, GROMACS 2025 Oct 19, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
NAMD script_API Control Colvars from scripts
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@giacomofiorin @fabsugar