[gmx-users] Documentation on gmx densorder?

[Eric Smoll]

Hello Micholas and David,

If possible, could this discussion be kept on the list.  I was unaware of
this tool and would like to know about "gmx densorder" input, output, and
usage.  If not, would it be OK if I sent my own followup questions to
Micholas or David in an independent email?

David, thank you for providing the reference to the list.  I will read it
before asking questions.

Best,
Eric

On Fri, Aug 31, 2018 at 6:15 AM Smith, Micholas D. <smithmd at ornl.gov> wrote:

> Thanks you for directing me to the paper. Before I switch to off-line
> questions, do you recall what his inputs needed to be? I keep getting the
> error:
>
> " Program:     gmx densorder, version 2016.3
> Source file: src/gromacs/gmxana/gmx_densorder.cpp (line 808)
>
> Fatal error:
> No or not correct number (2) of output-file-series: 1
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> "
>
> When I add the flag -Spect or -or after it finishes reading my trr file.
>
> Thank you,
>
> Micholas
>
>
>
> ===================
> Micholas Dean Smith, PhD. MRSC
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van
> der Spoel <spoel at xray.bmc.uu.se>
> Sent: Friday, August 31, 2018 5:46 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Documentation on gmx densorder?
>
> Den 2018-08-30 kl. 15:34, skrev Smith, Micholas D.:
> > Dear GMX users,
> >
> >
> > I was wondering if anyone has used the gmx densorder (originally
> g_densorder) in the past utility in the past. I have system with an
> interface and the idea of "
> >
> > gmx densorder reduces a two-phase density distribution along an axis,
> computed
> > over a MD trajectory, to 2D surfaces fluctuating in time, by a fit to a
> > functional profile for interfacial densities" seems rather interesting.
> However, I haven't found any more documentation on this tool (i.e. what the
> binary format of its output is actually used for).
> >
> >
> > If anyone has used it and has some pointers on what the output should be
> read with, or remembers the paper(s) it originated from it would be quite
> useful.
>
> Guilty as charged:
> https://pubs.acs.org/doi/abs/10.1021/ct500459x
> It was the student who implemented the code and used it however, but
> feel free to contact me off line if you have more questions.
> >
> >
> > Thanks,
> >
> >
> > Micholas
> >
> >
> > ===================
> > Micholas Dean Smith, PhD. MRSC
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
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