GROMACS version: 2020.4
GROMACS modification: No
I am interested in studying interactions between a model lipid bilayer and a compound. In order to speed up the simulation I am planning to use Hydrogen Mass Repartitioning for the lipids. Should I also perform HMR for the interacting compound? Can a mixed simulation with HMR for lipids and no HMR for the compound be performed?
The whole system needs to have hydrogen masses repartitioned.
This mass redistribution is performed to decrease the frequency / speed of movement of the fastest moving atoms/bonds in the system, which is the lightest atoms (hydrogen). So if you only redistribute the mass of one set of molecules and leave another set, then the latter will still have the same set of fast/high frequency movement and you will not be able to use a longer time step i.e. you will achieve nothing.
Thank you Dr. Lemkul and Dr_DBW for the clarification.
Dear Dr. Lemkul, Dr_DBW and Gromacs community,
I tried building the HMR membrane using CHARMM-GUI with CHARMM36 FF. The hydrogen and carbon masses of the lipid and protein were increased/decreased as expected (hydrogen mass increased to 3.024 and carbon mass decreased depending on nummber of hydrogen attached to it) but the hydrogen mass remained at 1.008 for the TIP3P water. As pointed above, shouldn’t the mass of hydrogen and oxygen be also changed in water?
If CHARMM-GUI does not produce the expected output, I suggest you contact their developers directly. But the mass of H and O in water is controlled via the use of
define = -DHEAVY_H in the
.mdp file in the CHARMM36 port. I do not know if the CHARMM-GUI files provide this option, but this is the way it’s normally handled in the CHARMM force field for GROMACS. Other species have to have their masses explicitly reset; water is controlled at the input file level rather than modifying the topology.