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Is it possible to add an option to output the final alignment between repeats detected by QuatSymm and used for the calculation of the reported TM-score and RMSD (just as is done in CE-Symm, for examp…
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Hello,
I was wondering if it would be possible to include alternative scores such as [M-score](https://doi.org/10.1093/bioinformatics/btw300) and [TM-score](https://seq2fun.dcmb.med.umich.edu//TM-sc…
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Hi,
I am trying to use OpenMM to run a metadynamics simulation, in which i would like to get the free energy during the dissemble of alpha-helix to random coil. Here is the code and error. Could yo…
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Dear all,
I am using eABF free energy method to calculate dimerization energy. For this I have divided the 1d CV space in different windows and did the simulations. Now I am having .czar.grad files a…
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I'm looking into recent xia2_regression failures, and have noticed a slight divergence between processing results on linux and mac. Traced this back to dials.refine, where the MCD algorithm appears to…
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Hi Luwei!
I am running the test example, apparently without errors. But this single protein is taking too long (over one hour). Also, while I am using a dedicated GPU (RTX-4090), its utilization is…
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`rdMolAlign.GetBestRMS` fails in some cases when computing the RMSD between a QM optimized and an OPLS optimized molecule. This happens for all the analysis computing the rmsd, see e.g. for swope anal…
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Hello developers!
I saw the format of types for training both CNN_score and CNN_affinity needs rmsd and affinity label, but I don't wanna train or use CNN_score in my work, so I am searching for ho…
RJ-Li updated
11 months ago
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Were trying to get an pae_interaction less that 10, but when we put the contig as A100-200/0 70-100 we get i_pae (we assume its the pae_interaction score) as around 26, but when we use contig of 70-10…
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Also discussed in https://github.com/Colvars/colvars/issues/358
- [ ] An interface passing atomic indexes, coordinates, velocities and forces from GPU-resident NAMD to GPU Colvars.
- [x] Support m…