plumed2

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Splitting plumed into multiple libraries

2

I would like to change a bit the install procedure for the distributed binaries (currently: MacPorts and conda) splitting plumed into multiple libraries. Separate libraries would be independently installable. I...

GiovanniBussi

Problems with rendering of new manual

8

I noticed some problem in the rendering of the manual for 2.7. In particular, these pages seem to be incorrectly interrupted: https://www.plumed.org/doc-v2.7/user-doc/html/_r_e_w_e_i_g_h_t__w_h_a_m.html https://www.plumed.org/doc-v2.7/user-doc/html/trieste-5.html etc (it seems the pattern is that...

GiovanniBussi

I noticed a weird minor bug in the sidebar of the documentation. If I build the user-doc locally it displays correctly:  Instead on the plumed website...

invemichele

Configure: Throw an error instead of a warning when ArrayFire cannot be used?

3

Hi, We run into some issues lately because we missed that ArrayFire couldn't be used at configure and only discovered that much later. ``` $ ./configure ... --enable-af_cpu=no --enable-af_cuda=yes --enable-af_ocl=no...

RemiLacroix-IDRIS

UPPER_WALLS or LOWER_WALLS and PBCs

2

It looks like applying PBCs on the difference between the current CV value and that of the wall might not be the correct thing to do. See [this post](https://groups.google.com/d/msgid/plumed-users/2161183f-2857-4bc5-866e-524dc713ab91n%40googlegroups.com?utm_medium=email&utm_source=footer) for...

GiovanniBussi

Pushing docs for a private fork not working with Github Actions

5

I am trying to use Github Action to generate and push a manual from my PLUMED 2 fork, similar as I have done using Travis in the past. I generated...

valsson

[Gromacs 2020.2] Issue when trying to run SAXS on GPU

6

Hello, One of our users ran into some issues when trying to run Gromacs 2020.2 patched with Plumed 2.6.1 while configuring SAXS to run on GPU (using the ArrayFire library)....

RemiLacroix-IDRIS

@valsson I had to remove some equations that were resulting in errors when moving to ubuntu 20, with a newer Latex version that is less forgiving. Changes are here: 7400767ab57da15d9907c14208c24882f89184a5...

GiovanniBussi

Fix tail corrections in gromacs?

4

It looks like the energy communicated by gromacs does not include long tail corrections. Maybe this should be fixed if possible? See [mailing list](https://groups.google.com/d/msgid/plumed-users/CAGBhpicEGTq%3DATN9P3%3DY05u4u51hyYLsY5A8mnA3eC%3DkhqO5Ew%40mail.gmail.com?utm_medium=email&utm_source=footer).

GiovanniBussi

How to use HREX to correctly calculate the free energy difference.

1

Dear Plumed team, I tried to use HREX to perform FEP-REST2. If we choose a heat region (using plumed partial_tempering), the topologies between different replicas are different. However, when calculating...

AnguseZhang