Ja. At least if I got a raise I could afford the therapy required after
looking at gmx_trjconv.c... :-P
Mark
On Nov 22, 2013 4:48 PM, "Bogdan Costescu" wrote:
> On Fri, Nov 22, 2013 at 4:27 PM, Mark Abraham
> wrote:
> > Anybody wanting to add functionality to trjconv will need to offer me a
> >
On Fri, Nov 22, 2013 at 4:27 PM, Mark Abraham wrote:
> Anybody wanting to add functionality to trjconv will need to offer me a
> raise along with it ;-)
The functionality should never be added to trjconv, independent of
your raise :) trjconv does trajectory (and structure files along the
way) con
Ja. At some point you need to run 50 grompp, so wanting the 50 preparation
phases to be bundled in a magic trjconv is not worth doing. One should want
an operation to get the 50 inputs, then a shell script that does the
preparation and grompp for each, looping over that script. A scriptable set
of
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 Abrah
On Thu, Nov 21, 2013 at 12:06 PM, James Starlight wrote:
> 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 t
Take a frame, apply editconf and genbox?
Mark
On Nov 20, 2013 6:40 AM, "James Starlight" 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 wa
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 t
