[gmx-users] Cannot obtain center-of-mass radial distribution using Gromacs 2016.1

[Mark Abraham]

Hi,

That functionality has been re-implemented, and is now invoked differently.
See
http://manual.gromacs.org/documentation/2016.1/user-guide/cmdline.html#id1

Mark

On Fri, Jan 13, 2017 at 6:18 PM Boning Wu <bw194 at scarletmail.rutgers.edu>
wrote:

> Dear Gromacs Users,
>
> I am running gromacs 2016.1 on a server. After the simulation, I want to
> obtain the center of mass rdf using the following command:
>
> gmx_mpi rdf -f prod.xtc -s prod.tpr -o rdf.xvg -com -rdf mol_com
>
> However I got an error:
>
> Program:     gmx rdf, version 2016.1
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
> Function:    void gmx::CommandLineParser::parse(int *, char **)
>
> Error in user input:
> Invalid command-line options
>     Unknown command-line option -com
>     Unknown command-line option -rdf
>
>
> I used to this command in previous versions like 4.5.5 or 5.0.4, but there
> is no problem. I also tried to remove -com and -rdf flag in the command,
> and than the program can calculate rdf ...
>
> Can anyone tell me what happened? And how could I obtain center of mass
> rdf?
>
> gmx_mpi version gives following information:
>
> GROMACS version:    2016.1
> Precision:          single
> Memory model:       64 bit
> MPI library:        MPI
> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:        disabled
> SIMD instructions:  AVX_256
> FFT library:        Intel MKL
> RDTSCP usage:       enabled
> TNG support:        enabled
> Hwloc support:      disabled
> Tracing support:    disabled
> ....
> Build OS/arch:      Linux 3.10.0-229.20.1.el7.x86_64 x86_64
> Build CPU vendor:   Intel
> Build CPU brand:    Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
> Build CPU family:   6   Model: 63   Stepping: 2
> .....
>
>
> Thank you,
> Boning Wu
> --
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