Hi everyone,
I hope you are doing well.
I am applying an external force using acceleration. The way I calculated force was F=ma and m was Nc * Mw. Subsequently, P is ma/(LyLz). Note there is a unit conversion as well which I did not mention but overall it is a simple calculation.
For better clarification, here is a brief on system geometry:
Ly = 3.1613 nm
Lz = 5.05434 nm
Nc = 624
Mw = 12.0107 g/mol
I get the pressure for an acceleration equaling to 1 nm/ps^2, and then I use it to get to my desired pressure.
In my simulation setup, I used these parameters as below:
freezegrps = P2 P1
freezedim = N Y Y N Y Y
acc-grps = P1 P2
accelerate = 0.06419455 0 0 -0.00013009 0 0
0.06419455 and 0.00013009 are equivalent to 50 MPa and 0.1 MPa, respectively.
I read through posts here, that acceleration was going to be abandoned in 2021-2022. Then, I noticed, it is not abandoned at all in latest versions of gromacs, such as 2023.5.
I have done two types of simulations using the same setup; one with the gromacs 2016.4, and the other with gromacs 2023.5. There is a noticeable difference between them. basically, the latter resulted in much more filtered water (~350), whereas the former led to ~80 water molecules.
So, I checked my simulation log file, and noticed both of them have one thing in common:
acc: 0.0617287 0 0 -0.00259593 0 0 -0.00246584 0 0
nfreeze:N Y Y N Y Y N N N
First thing that is questionable here is that the first component of the first two acc sets is not the same as what I put in the mdp file. Could anyone please help me with this to understand better?
The next mysterious thing is that what is this -0.00246584 0 0? Is it for the other groups which are not under acceleration and freezing? If yes, why it is negative? I mean it should not be negative because the right hand of the system is under 50 MPa, while the other side is under 0.1 MPa.