Metadynamics calculations: Difference between revisions
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#If needed, define the bias potential in the {{FILE|PENALTYPOT}}-file | #If needed, define the bias potential in the {{FILE|PENALTYPOT}}-file | ||
The actual time-dependent bias potential is written to the {{FILE|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE|HILLSPOT}} to {{FILE|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>. | The actual time-dependent bias potential is written to the {{FILE|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE|HILLSPOT}} to {{FILE|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE|REPORT}}-file, check the lines after the string <tt>[[Metadynamics|Metadynamics]]</tt>. | ||
=== Nose-Hoover thermostat === | === Nose-Hoover thermostat === | ||
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== Related tags and sections == | == Related tags and sections == | ||
[[Metadynamics]] | {{FILE|ICONST}}, {{TAG|HILLS_H}}, {{TAG|HILLS_W}}, {{TAG|HILLS_BIN}}, {{FILE|PENALTYPOT}}, {{FILE|HILLSPOT}}, {{FILE|REPORT}} | ||
[[Metadynamics]], [[Nuclephile_Substitution_CH3Cl_-_mMD3 | Nucleophilic substitution of chloromethane by chloride using metadynamics]] | |||
<references/> | <references/> | ||
Latest revision as of 15:07, 28 May 2026
Anderson thermostat
- For a metadynamics run with Andersen thermostat, one has to:
- Set the standard MD-related tags: IBRION=0, TEBEG, POTIM, and NSW
- Set MDALGO=1 (MDALGO=11 in VASP 5.x), and choose an appropriate setting for ANDERSEN_PROB
- Set the parameters HILLS_H, HILLS_W, and HILLS_BIN
- Define collective variables in the ICONST-file, and set the
STATUSparameter for the collective variables to 5 - If needed, define the bias potential in the PENALTYPOT-file
The actual time-dependent bias potential is written to the HILLSPOT-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the PENALTYPOT-file. For the continuation of a metadynamics run, copy HILLSPOT to PENALTYPOT. The values of all collective variables for each MD step are listed in REPORT-file, check the lines after the string Metadynamics.
Nose-Hoover thermostat
- For a metadynamics run with Nose-Hoover thermostat, one has to:
- Set the standard MD-related tags: IBRION=0, TEBEG, POTIM, and NSW
- Set MDALGO=2 (MDALGO=21 in VASP 5.x), and choose an appropriate setting for SMASS
- Set the parameters HILLS_H, HILLS_W, and HILLS_BIN
- Define collective variables in the ICONST-file, and set the STATUS parameter for the collective variables to 5
- If needed, define the bias potential in the PENALTYPOT-file
The actual time-dependent bias potential is written to the HILLSPOT-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the PENALTYPOT-file. For the continuation of a metadynamics run, copy HILLSPOT to PENALTYPOT. The values of all collective variables for each MD step are listed in REPORT-file, check the lines after the string Metadynamics.
Related tags and sections
ICONST, HILLS_H, HILLS_W, HILLS_BIN, PENALTYPOT, HILLSPOT, REPORT
Metadynamics, Nucleophilic substitution of chloromethane by chloride using metadynamics