[gmx-users] Flat bottom position restraints
joewugromacs at gmail.com
Wed Jul 11 09:42:56 CEST 2018
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
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
; 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
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?
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