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, [email protected] <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <[email protected]> > Subject: Re: [gmx-users] error: Cannot compile and link MPI code with > mpicc > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected] <mailto:[email protected] > >> > > Subject: Re: [gmx-users] error: Cannot compile and link MPI code with > > mpicc > > To: Discussion list for GROMACS users <[email protected] > > <mailto:[email protected]>> > > Message-ID: > > <[email protected] > > <mailto:[email protected] > >> > > 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 <[email protected]> > Subject: Re: [gmx-users] Re : MPI > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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" <[email protected]> > Subject: [gmx-users] H2 topology > To: [email protected] > Cc: [email protected] > Message-ID: <[email protected]> > 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 <[email protected]> > Subject: Re: [gmx-users] H2 topology > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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. > [email protected] [email protected] http://folding.bmc.uu.se > > > ------------------------------ > > Message: 5 > Date: Mon, 1 Feb 2010 12:16:02 +0000 > From: Catarina Nunes <[email protected]> > Subject: [gmx-users] tutorial for ionic liquid > To: [email protected] > Message-ID: > <[email protected]> > 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" <[email protected]> > Subject: Re: [gmx-users] tutorial for ionic liquid > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected]> > Subject: [gmx-users] non-equilibrium MD simulations > To: [email protected] > Message-ID: <[email protected]> > 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 . > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100201/ff079c22/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Mon, 01 Feb 2010 08:08:02 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] non-equilibrium MD simulations > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 > [email protected] > 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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