[gmx-users] Documentation on gmx densorder?

[Smith, Micholas D.]

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.
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