Re: [gmx-users] Fwd: Residue 1 mapping problem?

[Justin Lemkul]

On 8/22/17 5:28 AM, morpheus wrote:

Thanks!


Is this also just a note or is there a problem?


"
WARNING 1 [file md_vsIonDod.mdp]:
   The sum of the two largest charge group radii (18.373196) is larger than
   rlist (1.40)
"

I found this on the gromacs webpage:

"A similar error ("The sum of the two largest charge group radii (X) is
larger than rlist") can arise under two circumstances:

1. The charge groups are inappropriately large or rlist is set too low.
2. Molecules are broken across periodic boundaries, which is not a
problem in a periodic system.  In this case, the sum of the two largest
charge groups will correspond to a value of twice the box vector along
which the molecule is broken."


If I visualise my protein with VMD nothing seems to be broken across the
box boundary ...


This seems to come up from grompp frequently and I can't figure out why 
(if nothing is truly broken across PBC).  It's totally irrelevant if 
you're using the Verlet cutoff scheme, since charge groups are ignored.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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==

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Re: [gmx-users] Average and bfactors.pdb

[Justin Lemkul]

On 8/21/17 5:25 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; } Hi justin
Thank you so much for replyingAccording to the gromacs tuturial, i am trying to 
analyse my complex in terms of RMSD. In order to do that, first it is needed to 
obtain the average structure to get RMSD vs average structure . And average 
structure is a side product of obtaining RMSF. Is there anyway that i can 
calculate RMSD instead of geting RMSD vs average structure? If you want to 
caculate RMSD , wont you perform this way?


I normally compute RMSD vs. the equilibrated structure or vs. the 
crystal structure, not an average structure.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] g_cluster

[Smolin, Nikolai]

Dear All,

I am using g_cluster. I am wondering what two groups used for?

group 1 for fit and RMSD calculation
group 2 for output

is g_cluster use RMSD values for clustering based on group 1 or group 2?


Any suggestions?

Thanks
Nikolai
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[gmx-users] 2nd CfP: From Virtual Reality to Immersive Analytics in Bioinformatics (SD 2018)

[Björn Sommer]

2nd CfP "From Virtual Reality to Immersive Analytics in Bioinformatics"

February 2018, Burlingame, California, USA
Special Session at the Stereoscopic Displays and Applications XXIX,
Burlingame, California
Special Issue of the Journal of Integrative Bioinformatics, vol 15, de
Gruyter Berlin


*Deadline Extension to September 10*
Although we already have a number of promising submissions, we would like to 
give you the opportunity to submit new abstracts, as the deadline for 
Electronic Imaging was extended. So we might aim now for a double session at 
SD!


Bioinformatics usually deals with the smallest entities of life,
therefore, visualization plays an important role in this field.
Stereoscopic rendering has already been used for a long time for
visualizing biological structures, dating back to the first hype of
virtual reality technologies 25 years ago when the CAVE was invented and
Head-Mounted Displays (HMD) became affordable. Triggered by the success
of new, modern HMDs such as Oculus Rift and HTC Vive, Virtual Reality
has recently gained a lot of attention again. On the other hand, a new
generation of large-scale "computational microscopes" is being
established, such as the CAVE2, representing large, nearly 360
degree-spanning visualization facilities.

At the same time, advanced "Visual Analytics" solutions have become an
important tool in all areas of scientific data analysis, combining
visualization, data mining and analysis methods, and user interaction.
Uniting both VR and VA, "Immersive Analytics" now starts to make use of
new technologies, immersing the scientist into the data, and, in the
best case, enabling advanced insights.

This special issue will focus on:
- What is the legacy of the past?
- Which approaches (partly) failed, and which success stories were
triggered
  by Virtual/Augmented Reality in the context of Bioinformatics?
- Which new ideas exist to approach now immersive analysis of biological
data?
- Which methods, technologies and/or applications are expected to change
  the way we see and perceive biology?

More info:
http://VR2IAinBioInf.immersive-analytics.org
 

Stereoscopic Displays and Applications XXIX, 28 Jan - 1 Feb 2018,
Burlingame, California

Since 1990, SD focuses on developments covering the entire
stereoscopic 3D imaging pipeline from capture, processing, and display,
to perception. SD XXIX will be held as part of the 2018 IS
International Symposium on Electronic Imaging: Science and Technology at
the Hyatt Regency San Francisco Airport, Burlingame, California, USA.
The conference brings together practitioners and researchers from
industry and academia to facilitate an exchange of current information
on stereoscopic imaging topics.
http://stereoscopic.org
 

Scope of the Special Session

Molecular biology produces huge amounts of data in the post-genomic era.
This includes data describing metabolic mechanisms and pathways,
structural genomic organization, patterns of regulatory regions;
proteomics, transcriptomics, and metabolomics. On the one hand, analysis
of this data uses essentially the methods and concepts of computer
science; on the other hand, the range of biological tasks solved by
researchers determines the range and scope of the data. Integrative
Bioinformatics is a new area of research using the tools of computer
science and electronic infrastructure applied to Biotechnology.

We solicit submissions that describe the use of Immersive Analytics for
data analysis in biology and Bioinformatics – potential topics include
(but are not limited to):
- Virtual and Augmented Reality approaches for data analysis
- Semi- and fully immersive data exploration
- Metabolic and Regulatory Network Modelling and Simulation
- Data Integration and Text Mining Approaches
- Signal Pathways and Cell Control
- Network Analysis
- Medical Informatics, Biomedicine and Biotechnology
- Integrative whole cell and molecular modelling
- Visual Analytics, Visualization, and Animation


Key Dates

- September 10, 2017: Extended Deadline: Abstract to SD 2018
- January 10, 2018: Full manuscript submission due to JIB
- February 1, 2018: Conference Presentation
- April 2018: Review and revision process finished
- May to June 2018: Publication of accepted papers


Organizers and Contact

- Bjorn Sommer, University of Konstanz, Konstanz/Monash University,
Melbourne
- Marc Baaden, Institut de Biologie Physico-Chimique, Paris
- Michael Krone, University of Stuttgart, Stuttgart
- Andrew Woods, Curtin University, Perth

If you have any question, please contact us:
vr2iainbio...@immersive-analytics.org
 

Journal of Integrative Bioinformatics

The Journal of Integrative Bioinformatics (JIB) is an international open
access journal publishing original peer-reviewed research articles
covering all aspects of integrative bioinformatics. It was established
in 2004 and joined the Open Access family of de Gruyter – one of the
oldest German publishers – in 2017. JIB (ISSN 

Re: [gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

[Carlos Navarro]

Hi Mark,
I’ll look in more detail the literature regarding this situation.
Thanks a lot for your reply.
Best,
Carlos

-- 
Carlos Navarro Retamal
Bioinformatic Engineering. PhD
Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations
Universidad de Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201  798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl

On August 23, 2017 at 10:23:03 AM, Mark Abraham (mark.j.abra...@gmail.com)
wrote:

Hi,

The emails have been arriving, but you're asking a complicated series of
questions. You need to find some literature that shows these protein and
lipid force fields were parameterized in a compatible way, and even then
you may need to show that you in fact get a physically reasonable result.
Only once you've got that sorted does integrating details like the atom
type descriptions into a hybrid forcefield folder become work worth doing.
We haven't written code to make "combine two *.ff folders" work smoothly,
because usually that's a nonsense operation...

Mark

On Wed, Aug 23, 2017 at 3:07 PM Carlos Navarro 
wrote:

> Dear gmx users,
>
> This is the third time I’m sending this email, but for some reason is not
> been accepted.
>
> I’m trying to set up a system consisting in a protein embebed into a
> bilayer. The whole system contains approximately ~40 atoms, so to
speed
> up the simulation I'm using virtual sites.
>
> I had no issue by converting my initial structure (protein) into a .gro+vs
> And for the lipid coordinates and parameters I’m using the one published
in
> the following article:
> http://pubs.acs.org/doi/pdfplus/10.1021/acs.jctc.5b01202 files here->
> https://zenodo.org/record/47649#.WZssiHeGMcg (In the link are the
> parameters for POPC, as well as the ffbonded and ffnonbonded for the
slipid
> forcefield).
>
> Unfortunately, since the lipids posses its own forcefield file (located in
> slipids.ff) I don’t how how to include the parameters in the ‘main’
> topology file, because if I do add the slipid forcefield in I get the
> following error:
>
> Fatal error:
>
> Syntax error - File forcefield.itp, line 5
>
> Last line read:
>
> '1 2 yes 0.5000 0.8333'
>
> Found a second defaults directive.
>
> error, which make sense.
> But also If I tried to add only the .itp file of POPCvs to the .top file
> gromacs complain about the atomtypes:
>
> ERROR 1 [file POPCvs.itp, line 66]:
>
> Atomtype MCH3N not found
>
>
> If I’m not mistaken, I have read some articles were people indeed can
> combine different forcefield, but sadly I don’t know how to do that.
> If this is imposible to do, does someone know vsite parameters for POPC
> that can be use in charmm36?
> Hope someone can help me.
> Best regards,
> Carlos
> --
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Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Mark Abraham]

Hi,

I don't understand whether you think diglycine is your solvent or your
solute.

Mark

On Tue, Aug 22, 2017 at 8:40 AM Dilip H N  wrote:

> Hello,
> 1] it is the solute+Diglycine which is the constituting the mixture...
> 2] the method to create the system for both were the same...
> the commands are...
> gmx editconf -f Diglycinechimera2.gro -o Diglybox.gro -c -box x y z
> (generating the box)
> gmx insert-molecules -f Diglybox.gro -ci abc.gro -nmol 10 -o Dglyabc.gro
> and for other system, gmx insert-molecules -f Diglybox.gro -ci def.gro
> -nmol 10 -o Dglydef.gro (adding the solute molecules and getting the final
> system)...
> here the two solute .gro files are abc.gro and def.groand i have
> followed the same procedure...
> and thn gmx pdb2gmx -f Dglyabc.gro (or) gmx pdb2gmx -f Dglydef.gro...there
> is [cmap] option in one topology file and in other topology there is no
> [cmap] option...
>
> How is it different thn..??
>
>
>
>
>
>
>  Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
>
> On Tue, Aug 22, 2017 at 11:49 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Your description is too confused to follow. Your use of the words solvent
> > and solute is unclear. pdb2gmx will never make a cmap that goes outside a
> > moleculetype.
> >
> > If one use of pdb2gmx made a cmap and the other did not, then they were
> > fundamentally different. If you don't know what was different, then you
> > aren't doing science because you don't know what your method was. If so,
> > start again and keep a record in a shell script this time.
> >
> > Mark
> >
> > On Tue, Aug 22, 2017 at 8:05 AM Dilip H N 
> > wrote:
> >
> > > 1] in the line 8231 [ Unknown cmap torsion between atoms 8 10 12 15 18]
> > it
> > > is the diglycine peptide molecule only, it is stating the atomic
> numbers
> > of
> > > the diglycine molecule (8,10,12,15) and solute molecule (18)
> > > 2] but one more problem is the Diglycine nitrogen and the solute
> > containing
> > > nitrogen are labelled as same (as N only)...
> > > ie., atoms 8,10,12,15 (here atom 10 is N, and other atoms are  C, CA)
> > > belong to diglycine and atom 18 belong to solute molecule of atom N,
> and
> > > hence i am getting the error...i hope so(But with other system tht
> i
> > > ran had no [cmap] in topology and the atoms in the solute were labelled
> > > differentlyand ran correctly..)
> > > 3] So can  i remove/delete the [cmap] line  (i tried removing cmap
> > line
> > > in topology..and thn with gmx grompp option it is workin fine..) does
> > that
> > > cause any error/manipulating the topology..etc..?? can i proceed
> removing
> > > [cmap] is thr any harm..?
> > > 4] I tried also with removing the last coloumn in [cmap] ie., removing
> > 18,1
> > > of am,funct..since as i told above the atom 18 is of the solute
> nitrogen
> > > molecule which is labelled as same in the .rtp file in charmmFF, which
> is
> > > causing the problemssince the gmx grompp is trying to bond wiht the
> > > atom 18 N  which is solute and not Diglycine (since both N's are
> labelled
> > > same)
> > > [ cmap ]
> > > ;  aiajakalam funct
> > > 810121518 1
> > > and edited and got it as:-
> > >
> > > [ cmap ]
> > > ;  aiajakal
> > > 8101215
> > > and thn now if i run gmx grompp -f min.mdp -c mixture.gro -p topol.top
> -o
> > > min.tpr
> > >  it is showing:-
> > >  WARNING 1 [file topol.top, line 8231]:
> > >   Too few parameters on line (source file
> > >
> > > /home/dilip/Downloads/gromacs-2016.2/src/gromacs/
> > gmxpreprocess/toppush.cpp,
> > > line 2198)
> > > So i tried with gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> > > min.tpr -maxwarn 2 , and now it is working fine...
> > >
> > > So i have tried with different options..and i have discussed what i
> have
> > > got..but are they the correct way...to proceed..??
> > >
> > > Any suggestions are welcome...
> > >
> > > Thank you...
> > >
> > >
> > >  Sent with Mailtrack
> > > <
> > > https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=22
> > > >
> > >
> > > On Mon, Aug 21, 2017 at 11:14 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > If your procedure for the two systems was actually the same, then the
> > > error
> > > > does not come from your solute. Unfortunately only you know what is
> on
> > > line
> > > > 8231... Work out what you did differently, e.g. by doing it again and
> > > > making sure you do it the same way.
> > > >
> > > > Mark
> > > >
> > > > On Mon, Aug 21, 2017 at 7:27 PM Dilip H N  >
> > > > wrote:
> > > >
> > > > > 1] I created Diglycine peptide from chimera software, and got the
> > .pdb
> > > > > file, added two different 

Re: [gmx-users] Extract only last frame from a trr

[Mark Abraham]

Hi,

That functionality would be convenient for you, but hasn't been written. I
suggest using gmx check to report on the details of the last frame, and use
that to construct input to trjconv.

Mark

On Tue, Aug 22, 2017 at 4:58 PM CLARK NICOLAS Joan 
wrote:

> Dear gmx users,
>
>
> Probably a silly question, but I have been having some trouble finding an
> answer.
>
>
> I would like to use trjconv to extract the last snapshot from the trr
> trajectory of a crashed simulation. Thing is, I want to do it with a script
> and without knowing exactly when the simulation crashed, so I am looking
> for an option in trjconv that makes it go directly to the last frame.
>
>
> Another way to do it, since my calculations crash due to LINCS WARNINGS
> (which I know the reason for), would be to gently terminate the calculation
> when I get the first warning and print the corresponding gro file.
>
>
> Is there any way to do it?
>
>
> Thanks,
>
> Joan
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> --
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Re: [gmx-users] Regarding indexing the atom labelled same in peptide

[Mark Abraham]

Hi,

The "1" selects the first index group, which is the whole peptide. If you
want to select the first residue, you have to use some other syntax.

Mark

On Tue, Aug 22, 2017 at 6:50 PM Dilip H N  wrote:

> Hello,
> I have a Diglycine peptide in .gro file as:-
> 1GLY  N1   1.312   0.940   1.100  0.5173  0.1852  0.2665
> 1GLY H12   1.375   1.015   1.064  0.3308 -0.2009 -0.8897
> 1GLY H23   1.376   0.860   1.115  2.0625  0.7372 -2.9245
> 1GLY H34   1.242   0.907   1.031  0.2385  0.6317  0.3326
> 1GLY CA5   1.240   0.963   1.228  0.3801 -0.0854  0.2381
> 1GLYHA16   1.155   0.898   1.233  1.2980 -1.3807 -0.5280
> 1GLYHA27   1.321   0.963   1.300 -1.1296 -1.6137  1.9682
> 1GLY  C  8   1.185   1.101   1.232  0.0318 -0.2122 -0.1516
> 1GLY  O9   1.171   1.174   1.133  0.1199  0.2166  0.1513
> 2GLY  N   10   1.148   1.148   1.352 -1.0777 -0.3721 -0.4264
> 2GLY HN   11   1.142   1.091   1.434 -0.1054  0.0667 -0.0362
> 2GLY CA   12   1.092   1.277   1.377  0.5476  0.2162  0.2355
> 2GLYHA1   13   1.170   1.351   1.365  0.3836  0.3441 -0.0427
> 2GLYHA2   14   1.012   1.294   1.306 -0.5941  1.1037  1.7136
> 2GLY  C   15   1.031   1.298   1.514  0.2354 -0.4348  0.1971
> 2GLYOT1   16   0.923   1.238   1.541  0.2601 -0.2386  0.7420
> 2GLYOT2   17   1.091   1.369   1.598  0.1878 -0.0650 -0.0813
>
> So now i want to index of the Nitrogen (N) of 1GLY only, but not N of
> 2GLY...
>
> I tried the the following command as:-
> gmx make_ndx -f abc.gro -o def.ndx
> 1 & a N
>
> But it is giving  2 Protein_&_N  : 2 atoms
> which is taking the N of 2GLY too into considerationwhich i don't
> required, I need the N of ...1GLY only
>
> So what is the correct command for this..??
>
> Thank you...
>
>
>
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>  Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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Re: [gmx-users] installation_server machine_error

[Mark Abraham]

Hi,

Please don't start new work with software that's no longer support and is
missing over four years worth of performance and correctness fixes. Some of
your problems relate to using commands that use the gmx wrapper binary,
which did not emerge until version 5.0.

Mark

On Wed, Aug 23, 2017 at 9:42 AM Kashif  wrote:

> dear sir
> after installing gromacs on server, I could not able to run the simulation.
> It always shows "-bash: command not found".
>  when I tried to locate the pdb2gmx, it showed the path as-
> /opt/apps/gromacs/4.6.6/bin/pdb2gmx_mpi
>
> When I run the following command by using the path as below--- I
> got error
>
> [kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx -f
> 1aki.pdb -o 1AKI_processed.gro -water spce
>
> -bash: /opt/apps/gromacs/4.6.6/bin/gmx: No such file or directory
>
> [kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/pdb2gmx -f 1aki.pdb
> -o
> 1AKI_processed.gro -water spce
>
> -bash: /opt/apps/gromacs/4.6.6/bin/pdb2gmx: No such file or directory
>
>
> Although after looking into the installed gromacs bin directory
> (/opt/apps/gromacs/4.6.6/bin), I found all the packages of gromacs...
>
> [root@Server bin]# ls
> completion.bash   g_dos_mpi  GMXRC.bash   g_sigeps_mpi
> completion.cshg_dyecoupl_mpi GMXRC.cshg_sorient_mpi
> completion.zshg_dyndom_mpi   GMXRC.zshg_spatial_mpi
> demux.pl  genbox_mpi g_nmeig_mpi  g_spol_mpi
> do_dssp_mpi   genconf_mpig_nmens_mpi  g_tcaf_mpi
> editconf_mpi  g_enemat_mpi   g_nmtraj_mpi g_traj_mpi
> eneconv_mpi   g_energy_mpi   g_options_mpig_tune_pme_mpi
> g_anadock_mpi genion_mpi g_order_mpi  g_vanhove_mpi
> g_anaeig_mpi  genrestr_mpi   g_pme_error_mpi  g_velacc_mpi
> g_analyze_mpi g_filter_mpi   g_polystat_mpi   g_wham_mpi
> g_angle_mpi   g_gyrate_mpi   g_potential_mpi  g_wheel_mpi
> g_bar_mpi g_h2order_mpi  g_principal_mpi  g_x2top_mpi
> g_bond_mpig_hbond_mpig_protonate_mpi  make_edi_mpi
> g_bundle_mpi  g_helix_mpig_rama_mpi   make_ndx_mpi
> g_chi_mpi g_helixorient_mpi  g_rdf_mpimd.log
> g_cluster_mpi g_hydorder_mpi g_rmsdist_mpimdrun_mpi
> g_clustsize_mpi   g_kinetics_mpi g_rmsf_mpi   mk_angndx_mpi
> g_confrms_mpi g_lie_mpi  g_rms_mpipdb2gmx_mpi
> g_covar_mpi   g_luck_mpi grompp_mpi   tpbconv_mpi
> g_current_mpi g_mdmat_mpig_rotacf_mpi trjcat_mpi
> g_density_mpi g_membed_mpi   g_rotmat_mpi trjconv_mpi
> g_densmap_mpi g_mindist_mpi  g_saltbr_mpi trjorder_mpi
> g_densorder_mpi   g_morph_mpig_sans_mpi   xplor2gmx.pl
> g_dielectric_mpi  g_msd_mpi  g_sas_mpixpm2ps_mpi
> g_dipoles_mpi gmxcheck_mpi   g_select_mpi
> g_disre_mpi   gmxdump_mpig_sgangle_mpi
> g_dist_mpiGMXRC  g_sham_mpi
>
>
> Kindly suggest me the proper commands so that I can run the simulation.
>
>
> regards
> kashif
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Re: [gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

[Mark Abraham]

Hi,

The emails have been arriving, but you're asking a complicated series of
questions. You need to find some literature that shows these protein and
lipid force fields were parameterized in a compatible way, and even then
you may need to show that you in fact get a physically reasonable result.
Only once you've got that sorted does integrating details like the atom
type descriptions into a hybrid forcefield folder become work worth doing.
We haven't written code to make "combine two *.ff folders" work smoothly,
because usually that's a nonsense operation...

Mark

On Wed, Aug 23, 2017 at 3:07 PM Carlos Navarro 
wrote:

> Dear gmx users,
>
> This is the third time I’m sending this email, but for some reason is not
> been accepted.
>
> I’m trying to set up a system consisting in a protein embebed into a
> bilayer. The whole system contains approximately ~40 atoms, so to speed
> up the simulation I'm using virtual sites.
>
> I had no issue by converting my initial structure (protein) into a .gro+vs
> And for the lipid coordinates and parameters I’m using the one published in
> the following article:
> http://pubs.acs.org/doi/pdfplus/10.1021/acs.jctc.5b01202 files here->
> https://zenodo.org/record/47649#.WZssiHeGMcg (In the link are the
> parameters for POPC, as well as the ffbonded and ffnonbonded for the slipid
> forcefield).
>
> Unfortunately, since the lipids posses its own forcefield file (located in
> slipids.ff) I don’t how how to include the parameters in the ‘main’
> topology file, because if I do add the slipid forcefield in I get the
> following error:
>
> Fatal error:
>
> Syntax error - File forcefield.itp, line 5
>
> Last line read:
>
> '1 2 yes 0.5000 0.8333'
>
> Found a second defaults directive.
>
> error, which make sense.
> But also If I tried to add only the .itp file of POPCvs to the .top file
> gromacs complain about the atomtypes:
>
> ERROR 1 [file POPCvs.itp, line 66]:
>
>   Atomtype MCH3N not found
>
>
> If I’m not mistaken, I have read some articles were people indeed can
> combine different forcefield, but sadly I don’t know how to do that.
> If this is imposible to do, does someone know vsite parameters for POPC
> that can be use in charmm36?
> Hope someone can help me.
> Best regards,
> Carlos
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[gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

[Carlos Navarro]

Dear gmx users,

This is the third time I’m sending this email, but for some reason is not
been accepted.

I’m trying to set up a system consisting in a protein embebed into a
bilayer. The whole system contains approximately ~40 atoms, so to speed
up the simulation I'm using virtual sites.

I had no issue by converting my initial structure (protein) into a .gro+vs
And for the lipid coordinates and parameters I’m using the one published in
the following article:
http://pubs.acs.org/doi/pdfplus/10.1021/acs.jctc.5b01202 files here->
https://zenodo.org/record/47649#.WZssiHeGMcg (In the link are the
parameters for POPC, as well as the ffbonded and ffnonbonded for the slipid
forcefield).

Unfortunately, since the lipids posses its own forcefield file (located in
slipids.ff) I don’t how how to include the parameters in the ‘main’
topology file, because if I do add the slipid forcefield in I get the
following error:

Fatal error:

Syntax error - File forcefield.itp, line 5

Last line read:

'1 2 yes 0.5000 0.8333'

Found a second defaults directive.

error, which make sense.
But also If I tried to add only the .itp file of POPCvs to the .top file
gromacs complain about the atomtypes:

ERROR 1 [file POPCvs.itp, line 66]:

  Atomtype MCH3N not found


If I’m not mistaken, I have read some articles were people indeed can
combine different forcefield, but sadly I don’t know how to do that.
If this is imposible to do, does someone know vsite parameters for POPC
that can be use in charmm36?
Hope someone can help me.
Best regards,
Carlos
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Re: [gmx-users] Missing values in enery EDR

[Mark Abraham]

Hi,

Check your log file, where it likely says that energy groups are not
supported on GPUs. Do a rerun on your traj you want to compute these things.

Mark

On Wed, 23 Aug 2017 12:08 Sergio Manzetti 
wrote:

> Hi, when running gmx energy on a simulation ouput, I get:
>
> ---
> 1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell.
> 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
> 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Potential
> 13 Pres.-DC 14 Pressure 15 Vir-XX 16 Vir-XY
> 17 Vir-XZ 18 Vir-YX 19 Vir-YY 20 Vir-YZ
> 21 Vir-ZX 22 Vir-ZY 23 Vir-ZZ 24 Pres-XX
> 25 Pres-XY 26 Pres-XZ 27 Pres-YX 28 Pres-YY
> 29 Pres-YZ 30 Pres-ZX 31 Pres-ZY 32 Pres-ZZ
> 33 #Surf*SurfTen 34 T-rest
>
>
> and there are many missing values, and should be like :
>
> ---
> 1 Angle 2 Proper-Dih. 3 Ryckaert-Bell. 4 Improper-Dih.
> 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR)
> 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy
> 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd
> 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX
> 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY
> 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ
> 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX
> 33 Pres-ZY 34 Pres-ZZ
> 35 #Surf*SurfTen 36 Coul-SR:PRB-PRB
> 37 LJ-SR:PRB-PRB 38 Coul-14:PRB-PRB
> 39 LJ-14:PRB-PRB 40 Coul-SR:PRB-SOL
> 41 LJ-SR:PRB-SOL 42 Coul-14:PRB-SOL
> 43 LJ-14:PRB-SOL 44 Coul-SR:PRB-NA 45 LJ-SR:PRB-NA 46 Coul-14:PRB-NA
> 47 LJ-14:PRB-NA 48 Coul-SR:PRB-CL 49 LJ-SR:PRB-CL 50 Coul-14:PRB-CL
> 51 LJ-14:PRB-CL 52 Coul-SR:PRB-DNA
> 53 LJ-SR:PRB-DNA 54 Coul-14:PRB-DNA
> 55 LJ-14:PRB-DNA 56 Coul-SR:SOL-SOL
> 57 LJ-SR:SOL-SOL 58 Coul-14:SOL-SOL
> 59 LJ-14:SOL-SOL 60 Coul-SR:SOL-NA 61 LJ-SR:SOL-NA 62 Coul-14:SOL-NA
> 63 LJ-14:SOL-NA 64 Coul-SR:SOL-CL 65 LJ-SR:SOL-CL 66 Coul-14:SOL-CL
> 67 LJ-14:SOL-CL 68 Coul-SR:SOL-DNA
> 69 LJ-SR:SOL-DNA 70 Coul-14:SOL-DNA
> 71 LJ-14:SOL-DNA 72 Coul-SR:NA-NA 73 LJ-SR:NA-NA 74 Coul-14:NA-NA
> 75 LJ-14:NA-NA 76 Coul-SR:NA-CL 77 LJ-SR:NA-CL 78 Coul-14:NA-CL
> 79 LJ-14:NA-CL 80 Coul-SR:NA-DNA 81 LJ-SR:NA-DNA 82 Coul-14:NA-DNA
> 83 LJ-14:NA-DNA 84 Coul-SR:CL-CL 85 LJ-SR:CL-CL 86 Coul-14:CL-CL
> 87 LJ-14:CL-CL 88 Coul-SR:CL-DNA 89 LJ-SR:CL-DNA 90 Coul-14:CL-DNA
> 91 LJ-14:CL-DNA 92 Coul-SR:DNA-DNA
> 93 LJ-SR:DNA-DNA 94 Coul-14:DNA-DNA
> 95 LJ-14:DNA-DNA 96 T-System 97 Lamb-System
>
>
>
> How can I try to recoved the missing values (the sim.mdp contains all
> groups in the tcl, so everything should work)?
>
> Thanks
> --
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[gmx-users] Missing values in enery EDR

[Sergio Manzetti]

Hi, when running gmx energy on a simulation ouput, I get: 

--- 
1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell. 
5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) 
9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Potential 
13 Pres.-DC 14 Pressure 15 Vir-XX 16 Vir-XY 
17 Vir-XZ 18 Vir-YX 19 Vir-YY 20 Vir-YZ 
21 Vir-ZX 22 Vir-ZY 23 Vir-ZZ 24 Pres-XX 
25 Pres-XY 26 Pres-XZ 27 Pres-YX 28 Pres-YY 
29 Pres-YZ 30 Pres-ZX 31 Pres-ZY 32 Pres-ZZ 
33 #Surf*SurfTen 34 T-rest 


and there are many missing values, and should be like : 

--- 
1 Angle 2 Proper-Dih. 3 Ryckaert-Bell. 4 Improper-Dih. 
5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 
9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 
13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 
17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 
21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 
25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 
29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 
33 Pres-ZY 34 Pres-ZZ 
35 #Surf*SurfTen 36 Coul-SR:PRB-PRB 
37 LJ-SR:PRB-PRB 38 Coul-14:PRB-PRB 
39 LJ-14:PRB-PRB 40 Coul-SR:PRB-SOL 
41 LJ-SR:PRB-SOL 42 Coul-14:PRB-SOL 
43 LJ-14:PRB-SOL 44 Coul-SR:PRB-NA 45 LJ-SR:PRB-NA 46 Coul-14:PRB-NA 
47 LJ-14:PRB-NA 48 Coul-SR:PRB-CL 49 LJ-SR:PRB-CL 50 Coul-14:PRB-CL 
51 LJ-14:PRB-CL 52 Coul-SR:PRB-DNA 
53 LJ-SR:PRB-DNA 54 Coul-14:PRB-DNA 
55 LJ-14:PRB-DNA 56 Coul-SR:SOL-SOL 
57 LJ-SR:SOL-SOL 58 Coul-14:SOL-SOL 
59 LJ-14:SOL-SOL 60 Coul-SR:SOL-NA 61 LJ-SR:SOL-NA 62 Coul-14:SOL-NA 
63 LJ-14:SOL-NA 64 Coul-SR:SOL-CL 65 LJ-SR:SOL-CL 66 Coul-14:SOL-CL 
67 LJ-14:SOL-CL 68 Coul-SR:SOL-DNA 
69 LJ-SR:SOL-DNA 70 Coul-14:SOL-DNA 
71 LJ-14:SOL-DNA 72 Coul-SR:NA-NA 73 LJ-SR:NA-NA 74 Coul-14:NA-NA 
75 LJ-14:NA-NA 76 Coul-SR:NA-CL 77 LJ-SR:NA-CL 78 Coul-14:NA-CL 
79 LJ-14:NA-CL 80 Coul-SR:NA-DNA 81 LJ-SR:NA-DNA 82 Coul-14:NA-DNA 
83 LJ-14:NA-DNA 84 Coul-SR:CL-CL 85 LJ-SR:CL-CL 86 Coul-14:CL-CL 
87 LJ-14:CL-CL 88 Coul-SR:CL-DNA 89 LJ-SR:CL-DNA 90 Coul-14:CL-DNA 
91 LJ-14:CL-DNA 92 Coul-SR:DNA-DNA 
93 LJ-SR:DNA-DNA 94 Coul-14:DNA-DNA 
95 LJ-14:DNA-DNA 96 T-System 97 Lamb-System 



How can I try to recoved the missing values (the sim.mdp contains all groups in 
the tcl, so everything should work)? 

Thanks 
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Re: [gmx-users] installation_server machine_error

[Vytautas Rakeviius]

Well it seams that you compiled Gromacs with mpi support so now you should run 
it with sth. like that: mpirun -np 1 /opt/apps/gromacs/4.6.6/bin/gmx 
pdb2gmx_mpi -f 1aki.pdb -o 1AKI_processed.gro -water spceRun:man mpirunfor more 
details.
On Wednesday, August 23, 2017, 10:42:47 AM GMT+3, Kashif 
 wrote:

dear sir
after installing gromacs on server, I could not able to run the simulation.
It always shows "-bash: command not found".
 when I tried to locate the pdb2gmx, it showed the path as-
/opt/apps/gromacs/4.6.6/bin/pdb2gmx_mpi

When I run the following command by using the path as below--- I
got error

[kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx -f
1aki.pdb -o 1AKI_processed.gro -water spce

-bash: /opt/apps/gromacs/4.6.6/bin/gmx: No such file or directory

[kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/pdb2gmx -f 1aki.pdb -o
1AKI_processed.gro -water spce

-bash: /opt/apps/gromacs/4.6.6/bin/pdb2gmx: No such file or directory


Although after looking into the installed gromacs bin directory
(/opt/apps/gromacs/4.6.6/bin), I found all the packages of gromacs...

[root@Server bin]# ls
completion.bash  g_dos_mpi          GMXRC.bash      g_sigeps_mpi
completion.csh    g_dyecoupl_mpi    GMXRC.csh        g_sorient_mpi
completion.zsh    g_dyndom_mpi      GMXRC.zsh        g_spatial_mpi
demux.pl          genbox_mpi        g_nmeig_mpi      g_spol_mpi
do_dssp_mpi      genconf_mpi        g_nmens_mpi      g_tcaf_mpi
editconf_mpi      g_enemat_mpi      g_nmtraj_mpi    g_traj_mpi
eneconv_mpi      g_energy_mpi      g_options_mpi    g_tune_pme_mpi
g_anadock_mpi    genion_mpi        g_order_mpi      g_vanhove_mpi
g_anaeig_mpi      genrestr_mpi      g_pme_error_mpi  g_velacc_mpi
g_analyze_mpi    g_filter_mpi      g_polystat_mpi  g_wham_mpi
g_angle_mpi      g_gyrate_mpi      g_potential_mpi  g_wheel_mpi
g_bar_mpi        g_h2order_mpi      g_principal_mpi  g_x2top_mpi
g_bond_mpi        g_hbond_mpi        g_protonate_mpi  make_edi_mpi
g_bundle_mpi      g_helix_mpi        g_rama_mpi      make_ndx_mpi
g_chi_mpi        g_helixorient_mpi  g_rdf_mpi        md.log
g_cluster_mpi    g_hydorder_mpi    g_rmsdist_mpi    mdrun_mpi
g_clustsize_mpi  g_kinetics_mpi    g_rmsf_mpi      mk_angndx_mpi
g_confrms_mpi    g_lie_mpi          g_rms_mpi        pdb2gmx_mpi
g_covar_mpi      g_luck_mpi        grompp_mpi      tpbconv_mpi
g_current_mpi    g_mdmat_mpi        g_rotacf_mpi    trjcat_mpi
g_density_mpi    g_membed_mpi      g_rotmat_mpi    trjconv_mpi
g_densmap_mpi    g_mindist_mpi      g_saltbr_mpi    trjorder_mpi
g_densorder_mpi  g_morph_mpi        g_sans_mpi      xplor2gmx.pl
g_dielectric_mpi  g_msd_mpi          g_sas_mpi        xpm2ps_mpi
g_dipoles_mpi    gmxcheck_mpi      g_select_mpi
g_disre_mpi      gmxdump_mpi        g_sgangle_mpi
g_dist_mpi        GMXRC              g_sham_mpi


Kindly suggest me the proper commands so that I can run the simulation.


regards
kashif
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[gmx-users] installation_server machine_error

[Kashif]

dear sir
after installing gromacs on server, I could not able to run the simulation.
It always shows "-bash: command not found".
 when I tried to locate the pdb2gmx, it showed the path as-
/opt/apps/gromacs/4.6.6/bin/pdb2gmx_mpi

When I run the following command by using the path as below--- I
got error

[kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx -f
1aki.pdb -o 1AKI_processed.gro -water spce

-bash: /opt/apps/gromacs/4.6.6/bin/gmx: No such file or directory

[kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/pdb2gmx -f 1aki.pdb -o
1AKI_processed.gro -water spce

-bash: /opt/apps/gromacs/4.6.6/bin/pdb2gmx: No such file or directory


Although after looking into the installed gromacs bin directory
(/opt/apps/gromacs/4.6.6/bin), I found all the packages of gromacs...

[root@Server bin]# ls
completion.bash   g_dos_mpi  GMXRC.bash   g_sigeps_mpi
completion.cshg_dyecoupl_mpi GMXRC.cshg_sorient_mpi
completion.zshg_dyndom_mpi   GMXRC.zshg_spatial_mpi
demux.pl  genbox_mpi g_nmeig_mpi  g_spol_mpi
do_dssp_mpi   genconf_mpig_nmens_mpi  g_tcaf_mpi
editconf_mpi  g_enemat_mpi   g_nmtraj_mpi g_traj_mpi
eneconv_mpi   g_energy_mpi   g_options_mpig_tune_pme_mpi
g_anadock_mpi genion_mpi g_order_mpi  g_vanhove_mpi
g_anaeig_mpi  genrestr_mpi   g_pme_error_mpi  g_velacc_mpi
g_analyze_mpi g_filter_mpi   g_polystat_mpi   g_wham_mpi
g_angle_mpi   g_gyrate_mpi   g_potential_mpi  g_wheel_mpi
g_bar_mpi g_h2order_mpi  g_principal_mpi  g_x2top_mpi
g_bond_mpig_hbond_mpig_protonate_mpi  make_edi_mpi
g_bundle_mpi  g_helix_mpig_rama_mpi   make_ndx_mpi
g_chi_mpi g_helixorient_mpi  g_rdf_mpimd.log
g_cluster_mpi g_hydorder_mpi g_rmsdist_mpimdrun_mpi
g_clustsize_mpi   g_kinetics_mpi g_rmsf_mpi   mk_angndx_mpi
g_confrms_mpi g_lie_mpi  g_rms_mpipdb2gmx_mpi
g_covar_mpi   g_luck_mpi grompp_mpi   tpbconv_mpi
g_current_mpi g_mdmat_mpig_rotacf_mpi trjcat_mpi
g_density_mpi g_membed_mpi   g_rotmat_mpi trjconv_mpi
g_densmap_mpi g_mindist_mpi  g_saltbr_mpi trjorder_mpi
g_densorder_mpi   g_morph_mpig_sans_mpi   xplor2gmx.pl
g_dielectric_mpi  g_msd_mpi  g_sas_mpixpm2ps_mpi
g_dipoles_mpi gmxcheck_mpi   g_select_mpi
g_disre_mpi   gmxdump_mpig_sgangle_mpi
g_dist_mpiGMXRC  g_sham_mpi


Kindly suggest me the proper commands so that I can run the simulation.


regards
kashif
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