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
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...
etc.
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.
-Justin
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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