[gmx-users] Flat bottom position restraints

[Kevin Boyd]

Hi,

The flat bottom potential acts in both directions out from the center you
specify, so you should only need one potential - see figure 4.14 in the
reference manual, panel A. Use a positive r value and positive force
constant.

Kevin

On Wed, Jul 11, 2018 at 6:09 AM, Joe Wu <joewugromacs at gmail.com> wrote:

> Yes I am!
>
> On Wed, Jul 11, 2018 at 5:47 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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> > >
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