GROMACS version: Release 2024.1
GROMACS modification: No
Dear Gromacs community
I am investigating how to carry out simulations using a time step equal to 4 fs. In the manual (whose publication date is Feb 28, 2024), I have read that this can be done using two different methods:
A) Applying mass repartitioning [1].
B) Applying virtual sites plus mass repartitioning [2].
The literature suggests that imposing constraints on the angles of hydrogen atoms makes it possible to increase the time step of the simulation [3, 4]. Imposing constraints on angles of hydrogen atoms is supported by GROMACS setting <<constraints=h-angles>>. However, I cannot see this approach mentioned in the documentation as a recommended way to achieve a 4 fs time step. Is there any reason why mass repartitioning/virtual sites are preferred over constraining hydrogen angles?
Thank you very much. With kind regards
[1] From the manual: mass-repartitioning-factor (…) With h-bonds constrained a factor of 3 will usually enable a time step of 4 fs.
[2] From the manual: Disregarding these very fast oscillations of period 13 fs, the next shortest periods are around 20 fs, which will allow a maximum time step of about 4 fs. Removing the bond-angle degrees of freedom from hydrogen atoms can best be done by defining them as virtual interaction sites instead of normal atoms. Whereas a normal atom is connected to the molecule with bonds, angles and dihedrals, a virtual site’s position is calculated from the position of three nearby heavy atoms in a predefined manner (see also sec. Virtual interaction sites (page 435)).For the hydrogens in water and in hydroxyl, sulfhydryl, or amine groups, no degrees of freedom can be removed, because rotational freedom should be preserved. The only other option available to slow down these motions is to increase the mass of the hydrogen atoms at the expense of the mass of the connected heavy atom.
[3] Mazur, A. Hierarchy of Fast Motions in Protein Dynamics. J. Phys. Chem. B 1998, 102, 473–479.
[4] Stocker, U.; Juchli, D.; van Gunsteren, W. F. Increasing the time step and efficiency of molecular dynamics simulations: optimal solutions for equilibrium simulations or structure refinement of large biomolecules. Molecular Simulation 2003, 29, 123–138.