[gmx-users] Artificial Restraint/Wall/Potential at box top

[Vitaly V. Chaban]

Is it not better to post-process the trajectory, trjconv, to obtain the
bilayer where you need it?

Restraints impact the simulation results and this impact is not always easy
to isolate.




On Wed, Oct 14, 2015 at 3:34 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You may want to consider the flat-bottomed position restraints in GROMACS 5
> and up.
>
> Mark
>
> On Wed, Oct 14, 2015 at 8:26 PM shivangi nangia <shivangi.nangia at gmail.com
> >
> wrote:
>
> > Hello,
> >
> > I have a system that contains 2000 CG POPC and 100 (21 AA) peptides.
> >
> > I want to apply  a dummy wall at the top of the box so that my peptides
> do
> > not jump out of the box via PBC and re-enter the box from the bottom and
> > stick to the bilayer.
> >
> > Is there a way to do that in GROMACS? distance restraint?
> >
> >
> > Kindly suggest.
> >
> > Thanks in advance,
> > sxn
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