Project ID: plumID:23.029
Name: An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations
Archive: https://zenodo.org/record/8192455/files/PLUMED_NEST_REPO.zip
Category: bio
Keywords: SAXS, SANS, SAS, metainference, proteins, nucleic-acid
PLUMED version: 2.9
Contributor: Federico Ballabio
Submitted on: 04 Aug 2023
Publication: F. Ballabio, C. Paissoni, M. Bollati, M. de Rosa, R. Capelli, C. Camilloni, Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations. Journal of Chemical Theory and Computation. 19, 8401–8413 (2023)

PLUMED input files

File Compatible with
GELSOLIN/SLC_OFF/plumed.dat tested on v2.9 tested on master
GELSOLIN/SLC_ON/plumed.dat tested on v2.9 tested on master
UP1_RNA/SLC_OFF/plumed.dat tested on v2.9 tested on master
UP1_RNA/SLC_ON/plumed.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:47:18

Project description and instructions
Included are the input files to perform a metainference calculation using SAXS data as restraints and our latest hybrid SAXS forward model. This model allows for the inclusion of a solvent layer correction term. The simulations are meant to be performed using GROMACS and multiple replicas in the case of GELSOLIN, while using a single replica in the case of UP1.

Submission history
[v1] 04 Aug 2023: original submission

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plumeDnest:23.029