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Atomify should be able to just visualize LAMMPS trajectories, XYZ files and other formats. Of course the internal computes/fixes won't work in this case (unless we use the LAMMPS machinery to store al…
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Newly requested atoms after a `cv reset` command in NAMD seem to give wrong colvar values under some circumstances. This might be due to outdated proxy data, and hence be fixed by 2009985e6ac71ecc0856…
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Dear Toni,
Can Metagui process output generated via colvar module (another option to Plumed software).
I would assume currently No.
Does it require changes? If you can guide me I would apprec…
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Hi,
I am trying to read a protein-ligand system PDB/PSF file with Parmed and It keeps failing with the following error message. I am attaching the PDB, PSF and par_oplsaa_aam.inp files.
Any su…
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Dear Colvar team,
I would like to inquire about Metadynamics simulation for a system, subjected to NPT set-up.
With Plumed there is an issue about handling virial contribution for NAMD (as per …
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See http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html for a format description.
Only atom and bond sections.
There is an example file [ala.psf](../tree/dev/data/ala3…
arose updated
7 years ago
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New directory structure:
`colvars/tests/_/.in`
By default, this is enough to run a test with default VMD/NAMD/LAMMPS input, eg:
`namd/tests/library/Common/test.namd`
Test dirs may contain an extra …
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This problem was observed by @akohlmey on all Colvars input tests, and is most likely due to `new`ed feature objects not being deallocated when an object is destroyed, because the vector containing th…
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When I do this:
```
let source_bucket = "src_bucket_name";
let dest_bucket = "dest_bucket_name";
let req = CopyObjectRequest {
bucket: dest_bucket.clone(),
copy_sou…