A Python package developed for the BSC-EAPM group to set up protein models calculations.
For instructions, please check the README file located in the dependencies folder.
A tutorial for basic usage is available in the docs folder:
A Python package to prepare PDB models for further calculations
License: GNU General Public License v3.0
A Python package developed for the BSC-EAPM group to set up protein models calculations.
For instructions, please check the README file located in the dependencies folder.
A tutorial for basic usage is available in the docs folder:
Ei!
estava intentant llençar unes MDs, i mentre preparava el codi en local amb la nova versió de gromacs (v2023.3), i fent servir prepare_protein, mhe trobat amb un error que potser el podeu incorporar en un futur.
A la hora de fer NPT, la opció que hi ha a prepare_protein per fer Pressure coupling es Berendsen. Quan intentes fer la npt amb la nova versió de Gromacs, et salta un fatal error, perque diu que NO sha de fer servir, i dona com a opció el C-rescale.
He mirat la docu, i sembla que efectivament, lhan fet deprecated perque thermodynamically no es correcte.
https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-value-pcoupl-Berendsen
Per production (ie md.mdp), esta posat un coupling correcte.
Es tan senzill com modificar el fitxer : prepare_proteins/scripts/md/gromacs/mdp/npt.mdp
For the md_analysis class, there is an attribute for the trajectory paths with no PBC. However, there is no one for the gro topology file. Could it be added?
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