[gmx-users] PCA tutorial
rituraj purohit
riturajpurohit at gmail.com
Tue Feb 2 04:52:51 CET 2010
Dear friends,
I want to do PCA for my MD data.
If anybody know the tutorial regarding PCA, please let me know.
Thanks in advanced
Regard
Rohan
On 2/1/10, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
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> Today's Topics:
>
> 1. Re: error: Cannot compile and link MPI code with mpicc
> (Mark Abraham)
> 2. Re: Re : MPI (Mark Abraham)
> 3. H2 topology (011013021-Jyotsna)
> 4. Re: H2 topology (David van der Spoel)
> 5. tutorial for ionic liquid (Catarina Nunes)
> 6. Re: tutorial for ionic liquid (Justin A. Lemkul)
> 7. non-equilibrium MD simulations (oguz gurbulak)
> 8. Re: non-equilibrium MD simulations (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 01 Feb 2010 22:32:35 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
> mpicc
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B66BBD3.3030408 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 01/02/10 20:19, Sarath Kumar wrote:
> >
> >
> > Message: 2
> > Date: Mon, 1 Feb 2010 12:31:32 +0530
> > From: Chandan Choudhury <iitdckc at gmail.com <mailto:iitdckc at gmail.com
> >>
> > Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
> > mpicc
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>>
> > Message-ID:
> > <4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3 at mail.gmail.com
> > <mailto:4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3 at mail.gmail.com
> >>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thanks.
> > I just added export CPPFLAGS=-I/usr/local/openmpi/include in the
> bashrc
> > file, and could compile the mpi version of gromacs.
> > The next thing is I got the error on executing mdrun_mpi -h
> > Following is the output. Kindly help.
> >
> > corsica:/usr/local/gromacs/bin # mdrun_mpi -h
> > [corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file
> > runtime/orte_init_stage1.c at line 182
> >
> --------------------------------------------------------------------------
> > It looks like orte_init failed for some reason; your parallel process
> is
> > likely to abort. There are many reasons that a parallel process can
> > fail during orte_init; some of which are due to configuration or
> > environment problems. This failure appears to be an internal
> failure;
> > here's some additional information (which may only be relevant to an
> > Open MPI developer):
> >
> > orte_rml_base_select failed
> > --> Returned value -13 instead of ORTE_SUCCESS
> >
> >
> --------------------------------------------------------------------------
> >
> --------------------------------------------------------------------------
> > It looks like MPI_INIT failed for some reason; your parallel process
> is
> > likely to abort. There are many reasons that a parallel process can
> > fail during MPI_INIT; some of which are due to configuration or
> > environment
> > problems. This failure appears to be an internal failure; here's
> some
> > additional information (which may only be relevant to an Open MPI
> > developer):
> >
> > ompi_mpi_init: orte_init_stage1 failed
> > --> Returned "Not found" (-13) instead of "Success" (0)
> >
> --------------------------------------------------------------------------
> > *** An error occurred in MPI_Init
> > *** before MPI was initialized
> > *** MPI_ERRORS_ARE_FATAL (goodbye)
> > [corsica:17130] Abort before MPI_INIT completed successfully; not
> > able to
> > guarantee that all other processes were killed!
> >
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
> >
> >
> >
> >
> > U will be getting error s like this
> > as the MPI failed.
> > When u run mdrun with MPI.
> > If u use this CPPFLAGS, and i also had a problem.
> > When i used this option, after that i was unable to revert back it to
> > the original state also.
> >
> > So the better option update the gcc, c++ compilers,
> > If u have doubt in this, remove gromacs, All MPi.
> >
> > then do yum install -y *openmpi*
> >
> > --It will automatically install the missing libraries in dependencies.
> >
> > and then download fftw ---latest
> >
> > the install fftw with
> > ./configure --enable-threads --enable-mpi
> > the gromacs
> > ./configure --enable-threads --enable-mpi
> >
> >
> > this will surely work, because in order gromacs work with MPI.
> > U should compile fftw with MPI as above.
>
> None of this will help if the MPI environment is not configured, e.g. a
> hostfile set up. Chandan needs to get a test MPI program to run before
> there is evidence any of this discussion belongs on the GROMACS mailing
> last.
>
> Mark
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 01 Feb 2010 22:34:06 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re : MPI
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B66BC2E.9090109 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 01/02/10 21:41, bharat gupta wrote:
> > hi all,
> > Can anyboddy tell me from where I can get full detail of MPI with
> > respect to GROMACS ..
>
> This question is too general. Please search the GROMACS website for
> whatever you're really searching for, and if that fails, ask a focussed
> question.
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 01 Feb 2010 15:27:58 +0530
> From: "011013021-Jyotsna" <011013021 at bioinfo.sastra.edu>
> Subject: [gmx-users] H2 topology
> To: gmx-users at gromacs.org
> Cc: jyots18888 at gmail.com
> Message-ID: <web-2479207 at sastra.edu>
> Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"
>
> Dear all,
>
> I want to run a simulation for an enzyme. It demands me to
> incorporate a Molecular hydrogen Topology with a dummy
> atom in between in the simulation in order to study the
> path of hydrogen in it.The problem is , the topology file
> I built induces many errors when i come to the energy
> minimization step. The version of gromacs I am using is
> 4.0. The topology file I built is as follows
>
>
>
> [ moleculetype ]
> ;name nrexcl
> H2 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr
> charge mass ; total charge
> 1 H 1 H2 H1 1
> 0.475 1.00800 ; 0.00
> 2 H 1 H2 H2 1
> 0.475 1.00800 ; 0.00
> 3 DUM 1 H2 DUM 1
> -0.950 0.000
>
> [ virtual_sites2 ]
> ; Site from funct a
> 3 1 2 1 0.7439756
>
>
> When ever I insert the hydrogen+dummy atom topology in the
> protein's .gro file, an error is generated regarding
> mismatch of residues or the dummy atom having mass 0 .
>
> I would be really grateful if anyone could provide me the
> hydrogen molecule topology and give some pointers towards
> it.
>
> Thank you,
>
> Jyotsna
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 01 Feb 2010 13:01:29 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] H2 topology
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B66C299.4080301 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2/1/10 10:57 AM, 011013021-Jyotsna wrote:
> > Dear all,
> >
> > I want to run a simulation for an enzyme. It demands me to incorporate a
> > Molecular hydrogen Topology with a dummy atom in between in the
> > simulation in order to study the path of hydrogen in it.The problem is ,
> > the topology file I built induces many errors when i come to the energy
> > minimization step. The version of gromacs I am using is 4.0. The
> > topology file I built is as follows
> >
> >
> >
> > [ moleculetype ]
> > ;name nrexcl
> > H2 3
> >
> > [ atoms ]
> > ; nr type resnr residu atom cgnr charge mass ; total charge
> > 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00
> > 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00
> > 3 DUM 1 H2 DUM 1 -0.950 0.000
> >
> > [ virtual_sites2 ]
> > ; Site from funct a
> > 3 1 2 1 0.7439756
> >
> >
> > When ever I insert the hydrogen+dummy atom topology in the protein's
> > .gro file, an error is generated regarding mismatch of residues or the
> > dummy atom having mass 0 .
> >
> > I would be really grateful if anyone could provide me the hydrogen
> > molecule topology and give some pointers towards it.
> >
>
> Please print the error message in your mail.
>
> Topology look OK, but you need to add a bond or constraint.
> Also the constant probably has to be 0.5 since you want the vsite in the
> center of the two atoms.
>
>
> > Thank you,
> >
> > Jyotsna
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 1 Feb 2010 12:16:02 +0000
> From: Catarina Nunes <cata.nunes at gmail.com>
> Subject: [gmx-users] tutorial for ionic liquid
> To: gmx-users at gromacs.org
> Message-ID:
> <a3cd35831002010416r4fcbecaawbac5b4895184b87d at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
> Do you have any tutorial for ?
> Best regards
> Catarina
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 01 Feb 2010 07:18:51 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] tutorial for ionic liquid
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B66C6AB.2070503 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Catarina Nunes wrote:
> > Dear all,
> > Do you have any tutorial for ?
> > Best regards
> > Catarina
>
> Gromacs tutorials can be found at:
>
> http://www.gromacs.org/Documentation/Tutorials
>
> If you don't find it there, try Google. If you don't find it there, it
> probably
> doesn't exist :)
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 1 Feb 2010 05:05:31 -0800 (PST)
> From: oguz gurbulak <gurbulakoguz at yahoo.com>
> Subject: [gmx-users] non-equilibrium MD simulations
> To: gmx-users at gromacs.org
> Message-ID: <547100.67241.qm at web36302.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All,
>
> I'm searching for a non-equilibrium MD tutorial done with Gromacs. Could
> you please help me to find a NEMD tutorial ?
>
> Thank in advance .
>
>
>
>
>
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> ------------------------------
>
> Message: 8
> Date: Mon, 01 Feb 2010 08:08:02 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] non-equilibrium MD simulations
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B66D232.3020307 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> oguz gurbulak wrote:
> > Dear All,
> >
> > I'm searching for a non-equilibrium MD tutorial done with Gromacs.
> > Could you please help me to find a NEMD tutorial ?
> >
>
> "Non-equilibrium" can encompass a variety of topics, so if you want
> specific
> advice, you'll have to be more specific. And, as I just mentioned to
> someone else:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-February/048498.html
>
> -Justin
>
> > Thank in advance .
> >
> >
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 70, Issue 5
> ****************************************
>
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