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" <jalem...@vt.edu> wrote: > On Thu, Nov 21, 2013 at 12:06 PM, James Starlight <jmsstarli...@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 > > jalem...@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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
