GROMACS modification: Yes/No
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Good day everyone!
I want to simulate an amyloid fibril spanning infinitely in the z direction and is able to interact with the periodic molecules only in the z direction. I have a few questions regarding this
Q 1. I turned on
periodic-molecules= yes and pbc = xy ( as described in the manual for infinite z systems);
but pbc = xy wouldn’t work. Some issue came up with the verlet cut-off scheme. and insists on nwalls=2 so that pcoupl and ewald sums would work. So, that won’t be good.
So as i understood from a recent work, (link below), i reverted back to pbc=xyz and gave more space in the x and y dimensions so that there won’t be any interactions in x and y dimensions. This is what i understood and is the only possibility. Is my approach correct?
Q 2: regarding box creation through editconf. the length of my fibril in z axis is 2.9 nm. Inorder to create a periodic system along z how should i create a box?
a) a box shorter than 2.9 nm say 2.5 nm? or
b) a box exactly at 2.9 nm ?
c) a box with 2.9 nm + 0.49 nm ? (corresponding to hydrogen bonds)
Comments/criticism would be valuable.