GROMACS version: 5.x
GROMACS modification: No
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Dear Gromacs users, could you please help me to understand:
if I vary the wall-density ( https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-wall-density ) how the some “atoms” in the wall are placed along the wall surface? Is it right, that total vdw potential of the wall is calculated as the superposition of potentials of the some “atoms”, that density whose density is given by wall-density in mdp file?
I tried to fininformation about the parameter “wall-density” in the manual, however there write very low about this parameter. Please, could anyone suggest, where I find more information about the how the vdw potetial of the wall is calculated and how it is depend of the “wall-density” parameter?
The are no actual atoms in the wall. The wall potential comes as an integral of potential of “atoms” smeared out over the surface of the wall. So we need factor in the potential that tells how many “atoms” there are per square nm. This simply scales the potential and gives the correct units.
I also asked a similar question.
Could you please tell me where one can read about the use of walls in simulations, since I could not find relevant information in the GROMACS manual and in other sources.
I thought there was a section about this in the reference manual, but there isn’t one (there should be though). It isn’t difficult to compute the integrals though, e.g. with the help of wolframalpha.