Re: [gmx-users] Tools for energy of solvation in polimers

[Justin Lemkul]

On 11/9/15 8:33 AM, Mishelle Oña wrote:

Hi, Yes I remember. However I only found that MM/PBSA could be done only with 
NAMD. Is it posible to make it in gromacs? Could you explain me a little bit 
how it works o any helpfull link?Mishelle



Google knows all about it.  There's a program and even a publication for you to 
read about it.  "GROMACS MMPBSA" turns it up.


-Justin


To: gmx-us...@gromacs.org
From: jalem...@vt.edu
Date: Mon, 9 Nov 2015 08:30:06 -0500
Subject: Re: [gmx-users] Tools for energy of solvation in polimers



On 11/9/15 8:18 AM, Mishelle Oña wrote:

   OK I understand, so you think I couldn´t use Gromacs to calculate the Energy 
of Solvation? If that is the case could you help me with a tutorial or other 
tipe of information that could help me with this staff. Please I have been 
struggling with this for weeks. I need to solve it


I already made such a recommendation:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101722.html

-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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Re: [gmx-users] periodic molecule

[Pierre-André Cazade]

Thanks a lot.

Regards,
Pierre

On 09/11/15 11:54, CHEN Pan wrote:

To set up an infinite cellulose chain, you need:

1): Set up" periodic_molecules = yes" in your mdp file.
2): Built the connection, such as bonds, angles, dihedrals and 1-4 pairs
between the last residue and the first residue in your topology file.
Infinite chain usually means the end of molecules is linked to itself,
which is the mirror of the head groups. You need to process by your own
script.

That's all. Good Luck!

2015-11-09 9:41 GMT+01:00 Pierre-André Cazade :


Dear GMX users,

I am currently simulating a system involving an infinite slab of
cellulose. To model it properly, I need each cellulose chain to be a
periodic molecule. I assume the keyword "periodic-molecule" is there to
provide such a feature. However, it is not clear from the manual how one
can build a periodic molecule. Does it require a particular residue
definition in the ff files or in the topology ones? What are the options
one must use with pdb2gmx and with grompp?

Thank you in advance for your help.

Best regards,
Pierre Cazade
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Re: [gmx-users] mpirun

[Justin Lemkul]

On 11/9/15 5:23 AM, Said wrote:

Hi,

I have a gateway access to uppmax. I could have copied 1aki.pdb to my
account using box.com since scp does not work.

when writing mpirun -np 1 pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water
spce,
it gives me an error with exit code: 225.



There is not point trying to run pdb2gmx with mpirun; preparation steps should 
usually be done interactively, ideally on a local machine, and the .tpr file 
sent to the cluster to execute mdrun.  Most preparation programs need some kind 
of interactive input, which can be scripted but it is not always obvious what 
needs to be done ahead of time, especially something as complex as pdb2gmx.


-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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Re: [gmx-users] Tools for energy of solvation in polimers

[Mishelle Oña]

Hi, Yes I remember. However I only found that MM/PBSA could be done only with 
NAMD. Is it posible to make it in gromacs? Could you explain me a little bit 
how it works o any helpfull link?Mishelle

> To: gmx-us...@gromacs.org
> From: jalem...@vt.edu
> Date: Mon, 9 Nov 2015 08:30:06 -0500
> Subject: Re: [gmx-users] Tools for energy of solvation in polimers
> 
> 
> 
> On 11/9/15 8:18 AM, Mishelle Oña wrote:
> >   OK I understand, so you think I couldn´t use Gromacs to calculate the 
> > Energy of Solvation? If that is the case could you help me with a tutorial 
> > or other tipe of information that could help me with this staff. Please I 
> > have been struggling with this for weeks. I need to solve it
> 
> I already made such a recommendation:
> 
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101722.html
> 
> -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
> 
> ==
> -- 
> Gromacs Users mailing list
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> * Please search the archive at 
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Re: [gmx-users] Tools for energy of solvation in polimers

[Justin Lemkul]

On 11/9/15 8:18 AM, Mishelle Oña wrote:

  OK I understand, so you think I couldn´t use Gromacs to calculate the Energy 
of Solvation? If that is the case could you help me with a tutorial or other 
tipe of information that could help me with this staff. Please I have been 
struggling with this for weeks. I need to solve it


I already made such a recommendation:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101722.html

-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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[gmx-users] Tools for energy of solvation in polimers

[Mishelle Oña]

 OK I understand, so you think I couldn´t use Gromacs to calculate the Energy 
of Solvation? If that is the case could you help me with a tutorial or other 
tipe of information that could help me with this staff. Please I have been 
struggling with this for weeks. I need to solve it 
 Mishelle

> > To: gmx-us...@gromacs.org
> > From: jalem...@vt.edu
> > Date: Sun, 8 Nov 2015 20:38:18 -0500
> > Subject: Re: [gmx-users] Free solvation, problems with g_bar
> > 
> > 
> > 
> > On 11/8/15 8:35 PM, Mishelle Oña wrote:
> > >   Hi everybody!I am calculating the energy of solvation of a polimer 
> > > (polilactic acid.) I have a simulation of 40 000 frames and I am taking 
> > > random frames of the simulation to aply the free energy tutorial of 
> > > gromacs. When I perform the g_bar tool this message:WARNING: Some of 
> > > these results violate the Second Law of Thermodynamics appears at the 
> > > end. Do you have any idea of what is wrong? or any advice about this 
> > > problem?
> > 
> > As I already told you several days ago, an alchemical transformation on a 
> > polymer is unlikely to converge or give sensible results.  You shouldn't 
> > approach your problem in this way.
> > 
> > -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
> > 
> > ==
> > -- 
> > Gromacs Users mailing list
> > 
> > * Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> > 
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> > a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] mpirun

[Samuel Flores]

Hi Justin,

Is gmx the same as ngmx?  Here are the binaries in the Uppmax gromacs directory:

[samuelf@tintin1 ~]$ ls /sw/apps/gromacs/4.6.3/tintin/bin/
GMXRCg_anadock_d  g_cluster  g_densorder_d   g_enemat   
g_helixorient_d  g_morph  g_pme_error_d  g_rmsdistg_select_d   g_traj   
 genbox  make_edi_d   trjcat_d
GMXRC.bash   g_anaeig g_cluster_dg_dielectricg_enemat_d 
g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangleg_traj_d 
 genbox_dmake_ndx trjconv
GMXRC.cshg_anaeig_d   g_clustsizeg_dielectric_d  g_energy   
g_hydorder_d g_msdg_polystat_d   g_rmsf   g_sgangle_d  
g_tune_pmegenconf make_ndx_d   trjconv_d
GMXRC.zshg_analyzeg_clustsize_d  g_dipoles   g_energy_d 
g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham   
g_tune_pme_d  genconf_d   mdruntrjorder
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_dg_disre g_filter_d 
g_lieg_nmeig_dg_principalg_rotacf_d   g_sigeps 
g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl
completion.zsh   g_angle_dg_covarg_disre_d   g_gyrate   
g_lie_d  g_nmens  g_principal_d  g_rotmat g_sigeps_d   g_velacc 
 genrestrmdrun_mpi_d  xplor2gmx.pl~
demux.pl g_barg_covar_d  g_dist  g_gyrate_d 
g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
g_velacc_dgenrestr_d  mk_angndxxpm2ps
do_dssp  g_bar_d  g_current  g_dist_dg_h2order  
g_luck_d g_nmtraj g_protonate_d  g_saltbr g_sorient_d  g_wham   
 gmxcheckmk_angndx_d  xpm2ps_d
do_dssp_dg_bond   g_current_dg_dos   g_h2order_d
g_mdmat  g_nmtraj_d   g_rama g_saltbr_d   g_spatialg_wham_d 
 gmxcheck_d  ngmx
editconf g_bond_d g_density  g_dos_d g_hbond
g_mdmat_dg_optionsg_rama_d   g_sans   g_spatial_d  g_wheel  
 gmxdump pdb2gmx
editconf_d   g_bundle g_density_dg_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_dg_helix
g_membed_d   g_order  g_rdf_dg_sasg_spol_d g_x2top  
 grompp  tpbconv
eneconv_dg_chig_densmap_dg_dyndomg_helix_d  
g_mindistg_order_dg_rms  g_sas_d  g_tcaf   
g_x2top_d grompp_dtpbconv_d
g_anadockg_chi_d  g_densorderg_dyndom_d  g_helixorient  
g_mindist_d  g_pme_error  g_rms_dg_select g_tcaf_d g_xrama  
 make_editrjcat


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  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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[gmx-users] DPPC hlothane Residue DPP not found in residue topology database

[Poncho Arvayo Zatarain]

Hello: Concerning about my last question of DPPC membrane and halothane 
simulation and the GROMOS 53a6. When i used pdb2gmx the following error 
appears: Residue DPP not found in residue topology database. Then, i googled to 
Gromacs webpage and i found XXX'_not_found_in_residue_topology_database. So, 
after that and because a suggestion that probably GROMOS53a6 is not the best 
stock for simulate membranes, i tried every option of forcefield that GROMACS 
presented to me: Amber93 protein Amber94 nucleic, Amber94 forcefield, Amber96 
protein nucleic Amber94, Amber99 protein nucleic Amber94, Amber99SB Protein, 
nucleic Amber 94, AmberGS forcefield, CHARMM27 all-atom forcefield, Gromos96 
43a1, 43a2, 45a3, 53a5, 53a6, 54a7 and OPLS-AA/L and the same error appears in 
every orcefield: Residue DPP not found in residue topology database. What can i 
do? Because i simulated an Apoferritin-halothane and DPPC membrane with water 
and used GROMOS5a6 and everything was fine, but not  this time.
Thanks
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Re: [gmx-users] DPPC hlothane Residue DPP not found in residue topology database

[Justin Lemkul]

On 11/9/15 1:11 PM, Poncho Arvayo Zatarain wrote:


Hello: Concerning about my last question of DPPC membrane and halothane 
simulation and the GROMOS 53a6. When i used pdb2gmx the following error 
appears: Residue DPP not found in residue topology database. Then, i googled to 
Gromacs webpage and i found XXX'_not_found_in_residue_topology_database. So, 
after that and because a suggestion that probably GROMOS53a6 is not the best 
stock for simulate membranes, i tried every option of forcefield that GROMACS 
presented to me: Amber93 protein Amber94 nucleic, Amber94 forcefield, Amber96 
protein nucleic Amber94, Amber99 protein nucleic Amber94, Amber99SB Protein, 
nucleic Amber 94, AmberGS forcefield, CHARMM27 all-atom forcefield, Gromos96 
43a1, 43a2, 45a3, 53a5, 53a6, 54a7 and OPLS-AA/L and the same error appears in 
every orcefield: Residue DPP not found in residue topology database. What can i 
do? Because i simulated an Apoferritin-halothane and DPPC membrane with water 
and used GROMOS5a6 and everything was fine, but not  this time.


Lipid residue names are 4 characters in most (all) force fields.  So your 
problem is very self-explanatory: it's wrong and needs to be changed to match 
the force field (whichever one you choose).


$ grep "DPP" *.ff/*.rtp
charmm36.ff/merged.rtp:[ DPPA ]
charmm36.ff/merged.rtp:[ DPPC ]
charmm36.ff/merged.rtp:[ DPPE ]
charmm36.ff/merged.rtp:[ DPPG ]
charmm36.ff/merged.rtp:[ DPPS ]
gromos43a1.ff/aminoacids.rtp:[ NDPP ]
gromos43a2.ff/aminoacids.rtp:[ NDPP ]
gromos45a3.ff/aminoacids.rtp:[ NDPP ]
gromos53a5.ff/aminoacids.rtp:[ NDPP ]
gromos53a5.ff/aminoacids.rtp:[ DPPC ]
gromos53a6.ff/aminoacids.rtp:[ NDPP ]
gromos53a6.ff/aminoacids.rtp:[ DPPC ]
gromos53a6_lipid.ff/aminoacids.rtp:[ NDPP ]
gromos53a6_lipid.ff/aminoacids.rtp:[ DPPC ]
gromos54a7.ff/aminoacids.rtp:[ NDPP ]
gromos54a7.ff/aminoacids.rtp:[ DPPC ]

Note that none of them say "DPP."

-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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Re: [gmx-users] mpirun

[Elsaid Younes]

Thank you!

On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores 
wrote:

> 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  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_trajgenbox  make_edi_d   trjcat_d
> >> GMXRC.bashg_anaeig g_cluster_dg_dielectricg_enemat_d
>  g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangle
> g_traj_d  genbox_dmake_ndx trjconv
> >> GMXRC.csh g_anaeig_d   g_clustsizeg_dielectric_d  g_energy
>  g_hydorder_d g_msdg_polystat_d   g_rmsf   g_sgangle_d
> g_tune_pmegenconf make_ndx_d   trjconv_d
> >> GMXRC.zsh g_analyzeg_clustsize_d  g_dipoles   g_energy_d
>  g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham
>  g_tune_pme_d  genconf_d   mdruntrjorder
> >> 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.cshg_angle  g_confrms_dg_disre
>  g_filter_d g_lieg_nmeig_dg_principalg_rotacf_d
>  g_sigeps g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl
> >> completion.zshg_angle_dg_covarg_disre_d
>  g_gyrate   g_lie_d  g_nmens  g_principal_d  g_rotmat
>  g_sigeps_d   g_velacc  genrestrmdrun_mpi_d  xplor2gmx.pl~
> >> demux.pl  g_barg_covar_d  g_dist  g_gyrate_d
>g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
> g_velacc_dgenrestr_d  mk_angndxxpm2ps
> >> 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_whamgmxcheckmk_angndx_d  xpm2ps_d
> >> do_dssp_d g_bond   g_current_dg_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_dg_optionsg_rama_d   g_sans   g_spatial_d
> g_wheel   gmxdump pdb2gmx
> >> editconf_dg_bundle g_density_dg_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_helixg_membed_d   g_order  g_rdf_dg_sas
> g_spol_d g_x2top   grompp  tpbconv
> >> eneconv_d g_chig_densmap_dg_dyndomg_helix_d
>   g_mindistg_order_dg_rms  g_sas_d  g_tcaf
>  g_x2top_d grompp_dtpbconv_d
> >> g_anadock g_chi_d  g_densorderg_dyndom_d
> g_helixorient  g_mindist_d  g_pme_error  g_rms_dg_select
>  g_tcaf_d g_xrama   make_editrjcat
> >>
> >>
> >> 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  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
> >>>
> >>> ==
> >>> --
> >>> 

Re: [gmx-users] mpirun

[Justin Lemkul]

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/
GMXRCg_anadock_d  g_cluster  g_densorder_d   g_enemat   
g_helixorient_d  g_morph  g_pme_error_d  g_rmsdistg_select_d   g_traj   
 genbox  make_edi_d   trjcat_d
GMXRC.bash   g_anaeig g_cluster_dg_dielectricg_enemat_d 
g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangleg_traj_d 
 genbox_dmake_ndx trjconv
GMXRC.cshg_anaeig_d   g_clustsizeg_dielectric_d  g_energy   
g_hydorder_d g_msdg_polystat_d   g_rmsf   g_sgangle_d  
g_tune_pmegenconf make_ndx_d   trjconv_d
GMXRC.zshg_analyzeg_clustsize_d  g_dipoles   g_energy_d 
g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham   
g_tune_pme_d  genconf_d   mdruntrjorder
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_dg_disre g_filter_d 
g_lieg_nmeig_dg_principalg_rotacf_d   g_sigeps 
g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl
completion.zsh   g_angle_dg_covarg_disre_d   g_gyrate   
g_lie_d  g_nmens  g_principal_d  g_rotmat g_sigeps_d   g_velacc 
 genrestrmdrun_mpi_d  xplor2gmx.pl~
demux.pl g_barg_covar_d  g_dist  g_gyrate_d 
g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
g_velacc_dgenrestr_d  mk_angndxxpm2ps
do_dssp  g_bar_d  g_current  g_dist_dg_h2order  
g_luck_d g_nmtraj g_protonate_d  g_saltbr g_sorient_d  g_wham   
 gmxcheckmk_angndx_d  xpm2ps_d
do_dssp_dg_bond   g_current_dg_dos   g_h2order_d
g_mdmat  g_nmtraj_d   g_rama g_saltbr_d   g_spatialg_wham_d 
 gmxcheck_d  ngmx
editconf g_bond_d g_density  g_dos_d g_hbond
g_mdmat_dg_optionsg_rama_d   g_sans   g_spatial_d  g_wheel  
 gmxdump pdb2gmx
editconf_d   g_bundle g_density_dg_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_dg_helix
g_membed_d   g_order  g_rdf_dg_sasg_spol_d g_x2top  
 grompp  tpbconv
eneconv_dg_chig_densmap_dg_dyndomg_helix_d  
g_mindistg_order_dg_rms  g_sas_d  g_tcaf   
g_x2top_d grompp_dtpbconv_d
g_anadockg_chi_d  g_densorderg_dyndom_d  g_helixorient  
g_mindist_d  g_pme_error  g_rms_dg_select g_tcaf_d g_xrama  
 make_editrjcat


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  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

Re: [gmx-users] mpirun

[Samuel Flores]

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  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_rmsdistg_select_d   
>> g_trajgenbox  make_edi_d   trjcat_d
>> GMXRC.bashg_anaeig g_cluster_dg_dielectricg_enemat_d 
>> g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangle
>> g_traj_d  genbox_dmake_ndx trjconv
>> GMXRC.csh g_anaeig_d   g_clustsizeg_dielectric_d  g_energy   
>> g_hydorder_d g_msdg_polystat_d   g_rmsf   g_sgangle_d  
>> g_tune_pmegenconf make_ndx_d   trjconv_d
>> GMXRC.zsh g_analyzeg_clustsize_d  g_dipoles   g_energy_d 
>> g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham   
>> g_tune_pme_d  genconf_d   mdruntrjorder
>> 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.cshg_angle  g_confrms_dg_disre g_filter_d 
>> g_lieg_nmeig_dg_principalg_rotacf_d   g_sigeps 
>> g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl
>> completion.zshg_angle_dg_covarg_disre_d   g_gyrate   
>> g_lie_d  g_nmens  g_principal_d  g_rotmat g_sigeps_d   
>> g_velacc  genrestrmdrun_mpi_d  xplor2gmx.pl~
>> demux.pl  g_barg_covar_d  g_dist  g_gyrate_d 
>> g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
>> g_velacc_dgenrestr_d  mk_angndxxpm2ps
>> do_dssp   g_bar_d  g_current  g_dist_dg_h2order  
>> g_luck_d g_nmtraj g_protonate_d  g_saltbr g_sorient_d  
>> g_whamgmxcheckmk_angndx_d  xpm2ps_d
>> do_dssp_d g_bond   g_current_dg_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_dg_optionsg_rama_d   g_sans   g_spatial_d  
>> g_wheel   gmxdump pdb2gmx
>> editconf_dg_bundle g_density_dg_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_dg_helix
>> g_membed_d   g_order  g_rdf_dg_sasg_spol_d 
>> g_x2top   grompp  tpbconv
>> eneconv_d g_chig_densmap_dg_dyndomg_helix_d  
>> g_mindistg_order_dg_rms  g_sas_d  g_tcaf   
>> g_x2top_d grompp_dtpbconv_d
>> g_anadock g_chi_d  g_densorderg_dyndom_d  g_helixorient  
>> g_mindist_d  g_pme_error  g_rms_dg_select g_tcaf_d 
>> g_xrama   make_editrjcat
>> 
>> 
>> 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  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
>>> 
>>> ==
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at 
>>> 

Re: [gmx-users] Problem with Charges

[Justin Lemkul]

On 11/9/15 12:04 PM, faride badalkhani wrote:

Dear all,
I have parameterized a relatively large molecule (136 atom) with PRODRG
server, and then I assigned charges and charge groups in a building bock
style manner. I know that my system include a total +8 charge, but when I
execute genbox command i receive the following note:

System total charge: 0.000

what should I do to overcome this problem?



What genbox reports means nothing.  It can't calculate charge from coordinates.

-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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[gmx-users] GROMACS 5.1.1 official release

[Mark Abraham]

Hi GROMACS users,

The official release of GROMACS 5.1.1 is available!

This release fixes some known bugs in 5.1, incorporates all fixes made in
the recent 5.0.7 release, and makes minor enhancements for
forward-compatibility for upcoming CUDA versions. We encourage all users of
5.1 to update to 5.1.1. Please see the link to the release notes below for
more details.

You can find the code, documentation, release notes, and test suite at the
links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.1.tar.gz
http://manual.gromacs.org/documentation/5.1.1/index.html (including
installation guide, user guide, reference manual)
http://manual.gromacs.org/documentation/5.1.1/ReleaseNotes/index.html
http://gerrit.gromacs.org/download/regressiontests-5.1.1.tar.gz

Happy simulating!

Mark Abraham
GROMACS development manager
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[gmx-users] per atom stress tensor from g_energy

[Moultos, Othon]

Dear all, I want to calculate the thermal conductivity of small molecules. I 
can see that I need heat current, J. J has a term Si which is the per atom 
stress tensor according to JPC, 141, 134101. Does anybody know how I can 
extract this term from the simulation with g_energy or any other tool. Thanks a 
lot in advance.

Otto
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Re: [gmx-users] mpirun

[Elsaid Younes]

Hi,

Thank you for your response.
When writing gmx, it gives the command not found. (Note I use windows)

Elsaid

On Mon, Nov 9, 2015 at 3:31 PM, Justin Lemkul  wrote:

>
>
> On 11/9/15 5:23 AM, Said wrote:
>
>> Hi,
>>
>> I have a gateway access to uppmax. I could have copied 1aki.pdb to my
>> account using box.com since scp does not work.
>>
>> when writing mpirun -np 1 pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water
>> spce,
>> it gives me an error with exit code: 225.
>>
>>
> There is not point trying to run pdb2gmx with mpirun; preparation steps
> should usually be done interactively, ideally on a local machine, and the
> .tpr file sent to the cluster to execute mdrun.  Most preparation programs
> need some kind of interactive input, which can be scripted but it is not
> always obvious what needs to be done ahead of time, especially something as
> complex as pdb2gmx.
>
> -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
>
> ==
> --
> Gromacs Users mailing list
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> posting!
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[gmx-users] Problem with Charges

[faride badalkhani]

Dear all,
I have parameterized a relatively large molecule (136 atom) with PRODRG
server, and then I assigned charges and charge groups in a building bock
style manner. I know that my system include a total +8 charge, but when I
execute genbox command i receive the following note:

System total charge: 0.000

what should I do to overcome this problem?

Truly yours,
Farideh
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Re: [gmx-users] mpirun

[Justin Lemkul]

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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[gmx-users] QM/MM

[Timofey Tyugashev]

I'm looking to try a QM/MM simulation for a protein-DNA system using 
Gussian09 & GROMACS 4.6 (these are available at the local cluster).
Does anyone has any experience working and getting results in this 
environment? Are there any notable problems? Should I pay special 
attention to any particular topics?

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34

[Peter Stern]

Hi,



All your links give me the following, so I can't see what errors you are 
getting:
403 Forbidden

JSP3/2.0.4



But, you don't have to renumber the atoms in your PDB file.  Gromacs ignores 
those numbers and uses its own numbers.  Otherwise, how could it deal with 
numbers over 99,999 which won't fit into the pdb file's I5 format for atom 
numbers?  And when pdb2gmx adds hydrogen atoms it obviously has to renumber the 
coordinates.  It is possible that by editing your pdb or gro files you are 
introducing errors, but I don't know.



Regards,

Peter Stern



-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ???
Sent: Monday, November 09, 2015 8:55 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34



Dear,

I did some operations on my pdb or gro format file, for example, I deleted some 
atoms randomly to mimic a hole, then I had to re-number atoms in the pdb or gro 
format file by my code. The re-new pdb or gro file like picture 1 LINK: 
http://d.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=81b1352c18178a82ca3c7fa5c63802b0/cefc1e178a82b90149070cd3758da9773812efac.jpg?referer=54bbeb0fafec8a134d0d63d04962=.jpg,

thengromacs given errors like below picture 2 LINK: 
http://e.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=aec123e3ce95d143de76e42643cbf33f/d833c895d143ad4b3d75892084025aafa50f06f3.jpg?referer=c2157104b51c87018fa186d66292=.jpg,

but, I wrote itp and n2t file actually and there were no errors when uesd in 
others pdb or gro format structure file below 9 atoms. I consulted pdb web, 
I found that pdb format file reset 100,000th atom`s number to zero, then I 
reset the 100,000th atom number to 0, it shows in below picture 3 LINK: 
http://h.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=2f6ce308ba3eb13540c7b7be9625d9ee/18d8bc3eb13533fa2ded5cceaed3fd1f40345bf3.jpg?referer=7d7df4241dd5ad6ef3ee50daa591=.jpg.

Gromacs given errors again when I run jobs showed in below picture 4 LINK: 
http://f.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=711787ced41b0ef468e8985bedff20e7/7c1ed21b0ef41bd578bb271457da81cb38db3d62.jpg?referer=ace4f085b519ebc4996f42a97b21=.jpg.

Thanks a lot.

> Message: 5

> Date: Sun, 08 Nov 2015 09:14:39 +

> From: Mark Abraham >

> To: gmx-us...@gromacs.org

> Subject: Re: [gmx-users] How to build a correct structure file beyond

>  9 atoms using pdb or gro extend format ?

> Message-ID:

>  
> 

[gmx-users] mpirun

[Said]

Hi,

I have a gateway access to uppmax. I could have copied 1aki.pdb to my
account using box.com since scp does not work.

when writing mpirun -np 1 pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water
spce,
it gives me an error with exit code: 225.

Elsaid
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Re: [gmx-users] mpirun

[Elsaid Younes]

Hi,

it gives me file input/output  error 1aki.pdb.

Elsaid

On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes  wrote:

> Thank you!
>
> On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores 
> wrote:
>
>> 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  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_trajgenbox  make_edi_d   trjcat_d
>> >> GMXRC.bashg_anaeig g_cluster_dg_dielectricg_enemat_d
>>g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangle
>> g_traj_d  genbox_dmake_ndx trjconv
>> >> GMXRC.csh g_anaeig_d   g_clustsizeg_dielectric_d  g_energy
>>g_hydorder_d g_msdg_polystat_d   g_rmsf   g_sgangle_d
>> g_tune_pmegenconf make_ndx_d   trjconv_d
>> >> GMXRC.zsh g_analyzeg_clustsize_d  g_dipoles   g_energy_d
>>g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham
>>  g_tune_pme_d  genconf_d   mdruntrjorder
>> >> 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.cshg_angle  g_confrms_dg_disre
>>  g_filter_d g_lieg_nmeig_dg_principalg_rotacf_d
>>  g_sigeps g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl
>> >> completion.zshg_angle_dg_covarg_disre_d
>>  g_gyrate   g_lie_d  g_nmens  g_principal_d  g_rotmat
>>  g_sigeps_d   g_velacc  genrestrmdrun_mpi_d  xplor2gmx.pl~
>> >> demux.pl  g_barg_covar_d  g_dist  g_gyrate_d
>>g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
>> g_velacc_dgenrestr_d  mk_angndxxpm2ps
>> >> 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_whamgmxcheckmk_angndx_d  xpm2ps_d
>> >> do_dssp_d g_bond   g_current_dg_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_dg_optionsg_rama_d   g_sans   g_spatial_d
>> g_wheel   gmxdump pdb2gmx
>> >> editconf_dg_bundle g_density_dg_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_helixg_membed_d   g_order  g_rdf_dg_sas
>> g_spol_d g_x2top   grompp  tpbconv
>> >> eneconv_d g_chig_densmap_dg_dyndomg_helix_d
>>   g_mindistg_order_dg_rms  g_sas_d  g_tcaf
>>  g_x2top_d grompp_dtpbconv_d
>> >> g_anadock g_chi_d  g_densorderg_dyndom_d
>> g_helixorient  g_mindist_d  g_pme_error  g_rms_dg_select
>>  g_tcaf_d g_xrama   make_editrjcat
>> >>
>> >>
>> >> 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  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

[gmx-users] periodic molecule

[Pierre-André Cazade]

Dear GMX users,

I am currently simulating a system involving an infinite slab of 
cellulose. To model it properly, I need each cellulose chain to be a 
periodic molecule. I assume the keyword "periodic-molecule" is there to 
provide such a feature. However, it is not clear from the manual how one 
can build a periodic molecule. Does it require a particular residue 
definition in the ff files or in the topology ones? What are the options 
one must use with pdb2gmx and with grompp?


Thank you in advance for your help.

Best regards,
Pierre Cazade
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[gmx-users] How to build a correct structure file beyond 99999 atoms using pdb or gro extend format ?

[田会全]

Dear,
I did some operations on my pdb or gro format file, for example, I deleted some 
atoms randomly to mimic a hole, then I had to re-number atoms in the pdb or gro 
format file by my code. The re-new pdb or gro file like picture 1 LINK: 
http://d.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=81b1352c18178a82ca3c7fa5c63802b0/cefc1e178a82b90149070cd3758da9773812efac.jpg?referer=54bbeb0fafec8a134d0d63d04962=.jpg,
 
then, gromacs given errors like below picture 2 LINK: 
http://e.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=aec123e3ce95d143de76e42643cbf33f/d833c895d143ad4b3d75892084025aafa50f06f3.jpg?referer=c2157104b51c87018fa186d66292=.jpg,
 
but, I wrote itp and n2t file actually and there were no errors when uesd in 
others pdb or gro format structure file below 9 atoms. I consulted pdb web, 
I found that pdb format file reset 100,000th atom`s number to zero, then I 
reset the 100,000th atom number to 0, it shows in below picture 3 LINK: 
http://h.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=2f6ce308ba3eb13540c7b7be9625d9ee/18d8bc3eb13533fa2ded5cceaed3fd1f40345bf3.jpg?referer=7d7df4241dd5ad6ef3ee50daa591=.jpg.
 
Gromacs given errors again when I run jobs showed in below picture 4 LINK: 
http://f.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=711787ced41b0ef468e8985bedff20e7/7c1ed21b0ef41bd578bb271457da81cb38db3d62.jpg?referer=ace4f085b519ebc4996f42a97b21=.jpg.
Thanks a lot.
>> Message: 5
>> Date: Sun, 08 Nov 2015 09:14:39 +000
>> From: Mark Abraham 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] How to build a correct structure file beyond
>>  9 atoms using pdb or gro extend format ?
>> Message-ID:
>>  

Re: [gmx-users] periodic molecule

[CHEN Pan]

To set up an infinite cellulose chain, you need:

1): Set up" periodic_molecules = yes" in your mdp file.
2): Built the connection, such as bonds, angles, dihedrals and 1-4 pairs
between the last residue and the first residue in your topology file.
Infinite chain usually means the end of molecules is linked to itself,
which is the mirror of the head groups. You need to process by your own
script.

That's all. Good Luck!

2015-11-09 9:41 GMT+01:00 Pierre-André Cazade :

> Dear GMX users,
>
> I am currently simulating a system involving an infinite slab of
> cellulose. To model it properly, I need each cellulose chain to be a
> periodic molecule. I assume the keyword "periodic-molecule" is there to
> provide such a feature. However, it is not clear from the manual how one
> can build a periodic molecule. Does it require a particular residue
> definition in the ff files or in the topology ones? What are the options
> one must use with pdb2gmx and with grompp?
>
> Thank you in advance for your help.
>
> Best regards,
> Pierre Cazade
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Pan Chen
Postdoctoral Associate
Tailor-Made Fuels from Biomass
AICES Graduate School
RWTH Aachen University
+49(0)241 8099205
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Re: [gmx-users] mpirun

[Justin Lemkul]

On 11/9/15 7:59 PM, Elsaid Younes wrote:

Hi,

it gives me file input/output  error 1aki.pdb.



The most likely explanation is that file doesn't exist in the working directory.

-Justin


Elsaid

On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes  wrote:


Thank you!

On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores 
wrote:


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  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_trajgenbox  make_edi_d   trjcat_d

GMXRC.bashg_anaeig g_cluster_dg_dielectricg_enemat_d

g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangle
g_traj_d  genbox_dmake_ndx trjconv

GMXRC.csh g_anaeig_d   g_clustsizeg_dielectric_d  g_energy

g_hydorder_d g_msdg_polystat_d   g_rmsf   g_sgangle_d
g_tune_pmegenconf make_ndx_d   trjconv_d

GMXRC.zsh g_analyzeg_clustsize_d  g_dipoles   g_energy_d

g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham
  g_tune_pme_d  genconf_d   mdruntrjorder

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.cshg_angle  g_confrms_dg_disre

  g_filter_d g_lieg_nmeig_dg_principalg_rotacf_d
  g_sigeps g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl

completion.zshg_angle_dg_covarg_disre_d

  g_gyrate   g_lie_d  g_nmens  g_principal_d  g_rotmat
  g_sigeps_d   g_velacc  genrestrmdrun_mpi_d  xplor2gmx.pl~

demux.pl  g_barg_covar_d  g_dist  g_gyrate_d

g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
g_velacc_dgenrestr_d  mk_angndxxpm2ps

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_whamgmxcheckmk_angndx_d  xpm2ps_d

do_dssp_d g_bond   g_current_dg_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_dg_optionsg_rama_d   g_sans   g_spatial_d
g_wheel   gmxdump pdb2gmx

editconf_dg_bundle g_density_dg_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_helixg_membed_d   g_order  g_rdf_dg_sas
g_spol_d g_x2top   grompp  tpbconv

eneconv_d g_chig_densmap_dg_dyndomg_helix_d

   g_mindistg_order_dg_rms  g_sas_d  g_tcaf
  g_x2top_d grompp_dtpbconv_d

g_anadock g_chi_d  g_densorderg_dyndom_d

g_helixorient  g_mindist_d  g_pme_error  g_rms_dg_select
  g_tcaf_d g_xrama   make_editrjcat



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  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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