[gmx-users] Expanding of the boundaries of the enssemble

[James Starlight]

Mark, does it possible to do such for the ensemble (each frame from the
trajectory) at one step ? For example I need to perform umbrella sampling
in 50 windows extracted from the initial trajectory expanding in each
umbrella window the Z dimension and add water to it.

James


2013/11/20 Mark Abraham <mark.j.abraham at gmail.com>

> Take a frame, apply editconf and genbox?
>
> Mark
> On Nov 20, 2013 6:40 AM, "James Starlight" <jmsstarlight at gmail.com> wrote:
>
> > Dear Gromacs Users,
> >
> > I have 10 snapshots of the MD trajectory in dcd format. Presently I'd
> like
> > to expand boundaries of my system (in all of that 10 conformers) in Z
> > dimension and add some water in upper and lower leaflets. Could you
> suggest
> > me most  easily way to do it having only trajectory and the topology as
> the
> > inputs?
> >
> >
> > James
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