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

Boning Wu bw194 at scarletmail.rutgers.edu
Fri Jan 13 18:18:35 CET 2017

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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