GROMACS version:
GROMACS modification: Yes/No
Hey,
Hope you all doing great.
I know for sure that when a group of atoms are frozen, the force corresponding to freezing affects the fluctuations contributing to pressure calculation.
So if it is the case, then surface tension also gets the impact as well, thereby hydrophilicity may not be as accurate as is expected.
I have read GROMACS manual and other forums about this matter. One solution is to use energy group exclusion implemented in GROMACS which is not supported in GROMACS 2020 and am not sure if it is supported in the latest version of GROMACS.
So, if I want to exclude should I just exclude the non-bonded interactions between frozen atoms? Or between frozen atoms and solvent/solute? The last one seems a bit non-sense to me because I suspect if I exclude the non-bonded interactions between frozen atoms and solvent/solute, then the effect of the nanosheet I have there will disappear.
I would be appreciative if you could give me your opinions regarding this.
Computing pressures with frozen atoms present is highly problematic. You want you frozen atoms to interact with the rest of the system, but the frozen atoms will experience stresses and how these are handled has large effects on the computed pressure.
Hi, thanks for your time.
So, hydrophilicity also gets affected? Because when pressure cannot be correct then the surface tension of liquid vapor also cannot be obtained correctly.
The hydrophilicity is not affected, but the computed surface tension will likely be incorrect.