colvars
colvars copied to clipboard
Colvars
Collective variables library for molecular simulation and analysis programs
Sometimes if I get a grad file like https://gist.github.com/HanatoK/cc03687d55caa6c9a730a3a01ef1de06, then it is not able to integrate by `abf_integrate`. The error message is: ``` ERROR: wrong coordinates in gradient file Expected...
Hi, When the latest devel version of NAMD was patched with the master (with downloaded lepton) version of Colvars, the compilation yielded the following error: `Make.depends:1: *** recipe commences before...
As mentioned in the conversation for #481, update the registry of output files to use a `std::map` rather than two paired lists, which are no longer worth using any more.
This is needed for correct handling of moving restraints (continuous, using targetNumSteps) that don't begin at step 0.
See #367 #407 and some messages in the [NAMD](https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0223.html) and [LAMMPS](https://matsci.org/t/re-lammps-users-jacobian-terms-in-the-colvar-package/41288) forums. Nothing too verbose or extensive is needed: users just ought to be aware that the term is present...
useful for restraint free energy perturbation: only efficient use of targetForceExponent. Draft because documentation is TODO. Closes #353
Right now targetForceExponent in restraints smoothes the lambda dependence of the force constant according to: kλ=k0+λ^α(k1−k0) , where k0, kλ, and k1 are the initial, current, and final values of...
@HanatoK Appending to files that already exist on disk is useful in some cases, but also rather fragile (for examples, when jobs crash and are restarted). @jhenin had already removed...
The minimum image code found in `position_distance()` assumes angles close to 90°. In one example, it fails with an angle at 72° and a distance a little smaller that the...