Haohao Fu

The latest (lepton) version causes compilation error of NAMD

5

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...

we should use Parrinello-Rahman barostat in Gromacs, as Berendsen barostat is generally thought to be bad

[feature request] interface for molecule > 200 atoms by submitting QM files

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- [ ] This is a feature request Dear LigParGen developers, I want to simulate a large organic molecule (>200 atoms), but current version of LigParGen can only deal with...

extended Lagrangian is not compatible with NAMD's globalMaster MTS

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Hi all, I recently found that extended-Lagrangian algorithms (e.g., eABF) are not compatible with NAMD's new globalMaster MTS. When running an eABF simulation with: ``` globalMasterFrequency 2 globalMasterScaleByFrequency off globalMasterStaleForces...

As mentioned in issues #874 and #649, this PR enables the use of a harmonic restraint as a collective variable (CV). This allows enhanced sampling algorithms to calculate the free-energy...

Non-reproducible PMF Output from Colvars Poisson Integrator

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Dear Jerome, [test_integrator.zip](https://github.com/user-attachments/files/21505734/test_integrator.zip) I encountered an unexpected discrepancy when using the default Poisson integrator in Colvars. After completing a 200-ns simulation (semi-eABF and the `czar.grad` files were adopted), I obtained...