[gmx-users] Flat bottom position restraints
joewugromacs at gmail.com
Wed Jul 11 12:09:35 CEST 2018
Yes I am!
On Wed, Jul 11, 2018 at 5:47 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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
> > sorts.
> > Or, if anyone can directly help out my case, I am trying to create two
> > 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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