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It would be useful to run one or more of the JACS benchmark relative transformation systems to get an idea for what kinds of problems we are likely to run into.
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I wish to utilize the amber99sb-disp force field in OpenMM, which is proficient in describing Intrinsically Disordered Proteins (IDPs). I intend to combine it with OpenMM's metadynamics to accelerate …
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Hi,
I ran a metadynamics simulation on strides of 100ns each using OpenMM v7.5.1 + Plumed v2.7. Although I can successfully restart my simulation and Plumed continues outputting data as it should, …
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Hi,
During executing the following command
`scatter(plot_feat[:,0],plot_feat[:,1],c=new_y.data.tolist(),cmap='jet')`
`xlim([-np.pi,np.pi])`
`ylim([-np.pi,np.pi])`
`cb` = plt.colorbar()
`xlab…
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Dear developers,
I'm working with 3 CV metadynamics with plummed and CP2K. Specifically, PLUMED: Version: 2.8.0 and CP2K version 2022.1.
I found your package when I tried to find the minimums.
I i…
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Dear developers,
I find some new features have been released without updating the documents.
1. Implicit Solvation
all available solvents have been extended to GFN-FF method since…
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The current sMD implementation allows to use RMSD, Distance and Torsion collective variables. I had a case where I had to use a custom function as one of my CVs ([plumed docs](https://www.plumed.org/d…
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When a `CustomCVForce` object contains a tabulated function whose parameters have been modified, calling `updateParametersInContext` works as expected. However, this fails in an analogous situation in…
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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-col…
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Dear Developers,
I wonder if you can implement the centro-sysmmetry parameter into PLUMED?
The parameter is defined as
$$
CSP = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2
$$
w…