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

[Mark Abraham]

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 tools that each do One Thing Well are much better than one magic tool
that can do exactly one complex thing.

Anybody wanting to add functionality to trjconv will need to offer me a
raise along with it ;-)

Mark
On Nov 21, 2013 6:30 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

> On Thu, Nov 21, 2013 at 12:06 PM, James Starlight <jmsstarlight at gmail.com
> >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 the Z dimension and add water to it.
> >
> >
> I can't think of any way to do this in one step, but it's trivial to
> script. There is no getting around the fact that you need to perform
> multiple manipulations on multiple configurations. Keep in mind that the
> resulting structures may not be topologically identical (number of waters
> may vary) so you will need a corresponding topology for each configuration,
> anyway.
>
> -Justin
>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>