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What appears here is a (very) outdated version of GROMACS, and usage needs to be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
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==================================================
Justin A. Lemkul, Ph.D.
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University of Maryland, Baltimore
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Baltimore, MD 21201
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
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