gromacs-fda
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HITS-MBM
Force Distribution Analysis (FDA) for GROMACS
Hello, the documentation of the vector2scalar option "norm" states that, > if it's **positive**, the vector force is oriented within -90 to 90 degrees with respect to the atoms/residues -...
Using a large index group (ndx-file) with indices larger than 1.000.000 the fda rerun aborts with: ``` ResidueRenumber: yes Vector2Scalar: norm Pairwise interactions selected: all Pairwise forces for groups: Protein...
Dear fda developers, I am trying to use gromacs-fda to calculate punctual stress during the course of a steered MD simulation. My input file looks like this onepair = summed...
Hello, I've installed fda on my school's hpc and am getting the following error: Program: gmx mdrun, version 2020.4-dev-20220124-df2cd772a-unknown Standard library runtime error (possible bug): (exception type: St13runtime_error) Unknown option...
I used `gmx_fda mdrun` to calculate pairwise forces between atoms (saved to out.pfa). Now I am trying to use `fda_get_stress` to calculate the punctual stress per atom from the pairwise...
I've used FDA code (v2021.7-fda2.11) to perform analysis on my polysaccharide system (SMD simulation). I've obtained .pfa and .pfr files. The scripts pfa_draw and pfa_loaduser are meant for both atom-based...
Could I get more context on what equation is used to calculate the virial? Is it \tau_{ij}, \tau_{ij}*\Omega , or just 0.5*\sum (r_{ij}^{l} - r_{ij}^{k})f_j^{kl} (https://en.wikipedia.org/wiki/Virial_stress) ?
