Hi everyone,
Do you have any idea how we can use
NPH ensemble in Gromacs?
Do we need to completely delete temperature coupling options and use Parrinello-Rahman as the barostat(or maybe c-rescale)?
Should any extra settings be considered?
Best
Ramin Ekhteiari Salmas
It is possible to run it in LAMMPS - look at the following link:
https://docs.lammps.org/fix_nph_body.html
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Jamoliddin Razzokov
Remove temperature coupling options: In the GROMACS input file (usually a .mdp file), you should remove any temperature coupling options such as tcoupl or tc-grps. This is because in the NPH ensemble, temperature is no longer explicitly controlled. Instead, it will be determined by the dynamics of the system. Use Parrinello-Rahman barostat: In the same .mdp file, set the barostat type to Parrinello-Rahman using the pcoupl or pcoupltype option. This barostat maintains a constant pressure in the system. For example: pcoupl = Parrinello-Rahman; You can specify additional parameters for the Parrinello-Rahman barostat, such as the reference pressure (ref-p) and compressibility (compressibility), according to your specific simulation requirements. Set the target pressure: Specify the desired target pressure using the ref-p = 1.0 option in the .mdp file. Additional considerations: Make sure your system is properly equilibrated before running the NPH ensemble simulation. It is also important to choose appropriate integration time steps and other simulation parameters based on your system and the properties you want to investigate.
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Farzane Jalalypour
You can always ask your GROMACS-related questions (only) on the GROMACS forum and get an answer directly from gmx experts:
https://gromacs.bioexcel.eu/
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