[gmx-users] Flat bottom position restraints

[Joe Wu]

Hi Justin (or anyone else who can help),

There was a post where Justin told us to look through the archive for
detailed steps as to how to set up flat bottom restraints, but I cannot
find it. I've been looking through the entire archive for that post where
he explains in detail. Can anyone help out with a link or a how-to?

For the skeptics out there, I've been googling:
site:https://mailman-1.sys.kth.se flat bottom restraint
site:https://mailman-1.sys.kth.se flat bottom position restraint
site:https://mailman-1.sys.kth.se flat bottomed restraint
site:https://mailman-1.sys.kth.se flat bottomed position restraint

I've gone through all the links and could not find any in-depth tutorial of
sorts.

Or, if anyone can directly help out my case, I am trying to create two flat
bottomed potentials acting in the +z and -z direction to keep my water
layer intact and un-evaporated. Above and below the water is vacuum. The
center of the water is at 2.7nm; and I would like the flat bottomed
potential to act 1.35nm above and below the water to keep it intact.

Currently, I have:

; Include water topology

#include "oplsaa.ff/spc.itp"

#ifdef POSRES

; Position restraint for each water oxygen

[ position_restraints ]

;  i funct       g         r(nm)       k

   1    2        5          1.35       -1000.0

   2    2        5          -1.35      1000.0

#endif
in addition to a restraint.gro file with the z-coordinate to read 2.7.

All that is happening when I load my TRR file on VMD is that the entire
system runs along the +z axis non-stop, unbounded by anything.

I will be glad to provide more information. Any kind souls?

Best,
Joe