[gmx-users] Flat bottom position restraints
mark.j.abraham at gmail.com
Wed Jul 11 11:48:03 CEST 2018
Are you telling grompp to use your restraint.gro?
On Wed, Jul 11, 2018 at 9:43 AM Joe Wu <joewugromacs at gmail.com> wrote:
> 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
> #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
> 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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