Recently I am learning how to choose md parameters and I encounter some problems.
1.According to gromacs manual of mdp options, “Run control - comm-mode” controls restriction on the center of mass motion. The default setting is “None”(so as the minim.mdp in “Lysozyme in water” tutorial), but I found some minim.mdp files in the paper which set “comm-mode = Linear” to remove center of mass translational velocity. I wonder when this approach should be adopted and why.
“Pressure coupling - refcoord_scaling” controls whether the reference coordinates for position restraints are scaled with the scaling matrix of the pressure coupling.
According to the manual, "no: The reference coordinates for position restraints are not modified. Note that with this option the virial and pressure will depend on the absolute positions of the reference coordinates.
all: The reference coordinates are scaled with the scaling matrix of the pressure coupling.
com: Scale the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The vectors of each reference coordinate to the center of mass are not scaled. Only one COM is used, even when there are multiple molecules with position restraints. For calculating the COM of the reference coordinates in the starting configuration, periodic boundary conditions are not taken into account. "
I noticed that some npt.mdp files choose “com” while some do not. I wonder when should we scale the reference coordinates and why.
The default setting for comm-mode is Linear, not None. Minimization is not a dynamical process, so there are no velocities, and therefore there is no need to remove net COM motion, which is a result of buildup of kinetic energy.
To be clear, the scaling is applied to the reference positions, not the coordinates during the simulation. Scaling is always required when using restraints, and the difference between all (each individual reference point is scaled, i.e. absolute coordinates) vs. com (everything scaled relative to the COM, i.e. relative coordinates) is probably negligible for most simulations, but com tends to be a bit more numerically stable.
@jalemkul, I found this post about mdp options for the lysozyme in water tutorial and I have a follow up question. I am also in my first year learning GROMACs and MM simulations :). The question I have is w.r.t to the mdp options files for npt.mdp and md.mdp. I am wondering why for the md.mdp production dynamics parameters this file still has the following:
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
Should pressure coupling still be on during production dynamics? And if so could you give a short explanation of why or point me to where I can read about maybe why? Thanks!
The terms NVT and NPT refer to the statistical mechanical ensembles under which the simulations are being performed. So the production .mdp file will have a barostat active as part of maintaining an NPT ensemble.
Great! Thanks for the response. I was nervous as when I was running Tinker bar program and the author indicates they use a third column for the trajectory box volumes for small adjustment to the U = PV term in the Gibbs free energy calculation. I am assuming GROMACs’ bar program does this too somehow based on your answer which is starting to make things come together logically. I haven’t really tested GROMAC’s bar yet other than to know it runs. I am comparing OPLS-AA in GROMAC’s vs AMOEBA in Tinker using these lambda state curves for electrostatic and vdw for alchemical FEP comparisons.