[gmx-users] Flat bottom position restraints

[Mark Abraham]

Hi,

Are you telling grompp to use your restraint.gro?

Mark

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
> 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
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