[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Justin Lemkul jalemkul at vt.edu
Sun Sep 4 19:51:25 CEST 2016

On 9/4/16 1:45 PM, Atila Petrosian wrote:
> Dear Mark,
> In /usr/local/gromasc/bin directory, there are only
> demux.pl
> gmx-completion.bash
> gmx-completion-gmx_mpi.bash
> gmx_mpi
> GMXRC.bash
> GMXRC.csh
> GMXRC.zshxplor2gmx.pl
> In this directory, there is gmx_mpi rather than gmx. It is true based
> on the http://manual.gromacs.org/documentation/5.1/ReleaseNotes/removed-features.html#removed-temporary-symlinks-from-pre-5-0-tool-names
> In above link:
> That period is now over, so gmx tool (or gmx_mpi tool) is the only way
> to use GROMACS in 5.1. The mdrun-only build will build mdrun (or
> mdrun_mpi as appropriate).
> But there are not any tool in /usr/local/gromacs/bin directory
> Are you sure the lack of tools such as pdb2gmx, editconf, mdrun,
> grompp and .... is not a problem ???

This is not a problem.

There is only one program now.  It is called gmx, or gmx_mpi if you enabled MPI. 
  Everything is now a module of the gmx program.

gmx pdb2gmx...
gmx grompp...


There are important changes to several tools, including re-naming and very 
different syntax.  Again, there is lots of documentation, mailing list 
discussion, and tutorial updates that are relevant here.


> I am confused. Please tell me hoe to use gromacs 5.1 tools.
> Best,
> Atila


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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