Oh that makes sense!
Elsaid, issue:
module load gromacs/5.0.4
"module load gromacs" defaults to an ancient release of gromacs.
Sam
On Nov 9, 2015, at 19:10, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/9/15 1:08 PM, Samuel Flores wrote:
Hi Justin,
Is gmx the same as ngmx? Here are the binaries in the Uppmax gromacs
directory:
gmx refers to the single binary provided as of 5.0, which is the new
setup. What appears here is a (very) outdated version of GROMACS, and usage
needs to be adjusted accordingly.
-Justin
[samuelf@tintin1 ~]$ ls /sw/apps/gromacs/4.6.3/tintin/bin/
GMXRC g_anadock_d g_cluster g_densorder_d
g_enemat g_helixorient_d g_morph g_pme_error_d g_rmsdist
g_select_d g_traj genbox make_edi_d trjcat_d
GMXRC.bash g_anaeig g_cluster_d g_dielectric g_enemat_d
g_hydorder g_morph_d g_polystat g_rmsdist_d g_sgangle
g_traj_d genbox_d make_ndx trjconv
GMXRC.csh g_anaeig_d g_clustsize g_dielectric_d g_energy
g_hydorder_d g_msd g_polystat_d g_rmsf g_sgangle_d
g_tune_pme genconf make_ndx_d trjconv_d
GMXRC.zsh g_analyze g_clustsize_d g_dipoles g_energy_d
g_kinetics g_msd_d g_potential g_rmsf_d g_sham
g_tune_pme_d genconf_d mdrun trjorder
completion.bash g_analyze_d g_confrms g_dipoles_d g_filter
g_kinetics_d g_nmeig g_potential_d g_rotacf
g_sham_d g_vanhove genion mdrun_d trjorder_d
completion.csh g_angle g_confrms_d g_disre
g_filter_d g_lie g_nmeig_d g_principal g_rotacf_d
g_sigeps g_vanhove_d genion_d mdrun_mpi xplor2gmx.pl
completion.zsh g_angle_d g_covar g_disre_d
g_gyrate g_lie_d g_nmens g_principal_d g_rotmat
g_sigeps_d g_velacc genrestr mdrun_mpi_d xplor2gmx.pl~
demux.pl g_bar g_covar_d g_dist g_gyrate_d
g_luck g_nmens_d g_protonate g_rotmat_d g_sorient
g_velacc_d genrestr_d mk_angndx xpm2ps
do_dssp g_bar_d g_current g_dist_d
g_h2order g_luck_d g_nmtraj g_protonate_d g_saltbr
g_sorient_d g_wham gmxcheck mk_angndx_d xpm2ps_d
do_dssp_d g_bond g_current_d g_dos g_h2order_d
g_mdmat g_nmtraj_d g_rama g_saltbr_d g_spatial
g_wham_d gmxcheck_d ngmx
editconf g_bond_d g_density g_dos_d g_hbond
g_mdmat_d g_options g_rama_d g_sans g_spatial_d
g_wheel gmxdump pdb2gmx
editconf_d g_bundle g_density_d g_dyecoupl g_hbond_d
g_membed g_options_d g_rdf g_sans_d g_spol
g_wheel_d gmxdump_d pdb2gmx_d
eneconv g_bundle_d g_densmap g_dyecoupl_d
g_helix g_membed_d g_order g_rdf_d g_sas
g_spol_d g_x2top grompp tpbconv
eneconv_d g_chi g_densmap_d g_dyndom g_helix_d
g_mindist g_order_d g_rms g_sas_d g_tcaf
g_x2top_d grompp_d tpbconv_d
g_anadock g_chi_d g_densorder g_dyndom_d
g_helixorient g_mindist_d g_pme_error g_rms_d g_select
g_tcaf_d g_xrama make_edi trjcat
Elsaid,
Regarding Justin’s suggestion, on Uppmax I believe the full path would
be:
source /sw/apps/gromacs/4.6.3/tintin/bin/GMXRC.bash
However I think you already issued
module load gromacs
which might source GMXRC .
Sam
On Nov 9, 2015, at 17:56, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/9/15 11:55 AM, Elsaid Younes wrote:
Hi,
Thank you for your response.
When writing gmx, it gives the command not found. (Note I use
windows)
Then you haven't configured your environment correctly.
http://www.gromacs.org/Documentation/Installation_Instructions_5.0#getting-access-to-gromacs-after-installation
-Justin
--
==================================================
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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==================================================
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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