Dear friends,<br>
I want to do PCA for my MD data.<br>
If anybody know the tutorial regarding PCA, please let me know.<br>
Thanks in advanced<br>
<br>
Regard<br>
Rohan<br>
<br>
<br>
On 2/1/10, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<div>
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<br> When replying, please edit your Subject line so it is more specific<br> than "Re: Contents of gmx-users digest..."<br> <br> <br> Today's Topics:<br> <br> 1. Re: error: Cannot compile and link MPI code with mpicc<br>
(Mark Abraham)<br> 2. Re: Re : MPI (Mark Abraham)<br> 3. H2 topology (011013021-Jyotsna)<br> 4. Re: H2 topology (David van der Spoel)<br> 5. tutorial for ionic liquid (Catarina Nunes)<br> 6. Re: tutorial for ionic liquid (Justin A. Lemkul)<br>
7. non-equilibrium MD simulations (oguz gurbulak)<br> 8. Re: non-equilibrium MD simulations (Justin A. Lemkul)<br> <br> <br> ----------------------------------------------------------------------<br> <br> Message: 1<br>
Date: Mon, 01 Feb 2010 22:32:35 +1100<br> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with<br> mpicc<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <<a href="mailto:4B66BBD3.3030408@anu.edu.au">4B66BBD3.3030408@anu.edu.au</a>><br> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br> On 01/02/10 20:19, Sarath Kumar wrote:<br> ><br> ><br> > Message: 2<br> > Date: Mon, 1 Feb 2010 12:31:32 +0530<br> > From: Chandan Choudhury <<a href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a> <mailto:<a href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a>>><br>
> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with<br> > mpicc<br> > To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br> > Message-ID:<br> > <<a href="mailto:4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3@mail.gmail.com">4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3@mail.gmail.com</a><br>
> <mailto:<a href="mailto:4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3@mail.gmail.com">4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3@mail.gmail.com</a>>><br> > Content-Type: text/plain; charset="iso-8859-1"<br>
><br> > Thanks.<br> > I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc<br> > file, and could compile the mpi version of gromacs.<br> > The next thing is I got the error on executing mdrun_mpi -h<br>
> Following is the output. Kindly help.<br> ><br> > corsica:/usr/local/gromacs/bin # mdrun_mpi -h<br> > [corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file<br> > runtime/orte_init_stage1.c at line 182<br>
> --------------------------------------------------------------------------<br> > It looks like orte_init failed for some reason; your parallel process is<br> > likely to abort. There are many reasons that a parallel process can<br>
> fail during orte_init; some of which are due to configuration or<br> > environment problems. This failure appears to be an internal failure;<br> > here's some additional information (which may only be relevant to an<br>
> Open MPI developer):<br> ><br> > orte_rml_base_select failed<br> > --> Returned value -13 instead of ORTE_SUCCESS<br> ><br> > --------------------------------------------------------------------------<br>
> --------------------------------------------------------------------------<br> > It looks like MPI_INIT failed for some reason; your parallel process is<br> > likely to abort. There are many reasons that a parallel process can<br>
> fail during MPI_INIT; some of which are due to configuration or<br> > environment<br> > problems. This failure appears to be an internal failure; here's some<br> > additional information (which may only be relevant to an Open MPI<br>
> developer):<br> ><br> > ompi_mpi_init: orte_init_stage1 failed<br> > --> Returned "Not found" (-13) instead of "Success" (0)<br> > --------------------------------------------------------------------------<br>
> *** An error occurred in MPI_Init<br> > *** before MPI was initialized<br> > *** MPI_ERRORS_ARE_FATAL (goodbye)<br> > [corsica:17130] Abort before MPI_INIT completed successfully; not<br> > able to<br>
> guarantee that all other processes were killed!<br> ><br> > --<br> > Chandan kumar Choudhury<br> > NCL, Pune<br> > INDIA<br> ><br> ><br> ><br> ><br> > U will be getting error s like this<br>
> as the MPI failed.<br> > When u run mdrun with MPI.<br> > If u use this CPPFLAGS, and i also had a problem.<br> > When i used this option, after that i was unable to revert back it to<br> > the original state also.<br>
><br> > So the better option update the gcc, c++ compilers,<br> > If u have doubt in this, remove gromacs, All MPi.<br> ><br> > then do yum install -y *openmpi*<br> ><br> > --It will automatically install the missing libraries in dependencies.<br>
><br> > and then download fftw ---latest<br> ><br> > the install fftw with<br> > ./configure --enable-threads --enable-mpi<br> > the gromacs<br> > ./configure --enable-threads --enable-mpi<br> ><br>
><br> > this will surely work, because in order gromacs work with MPI.<br> > U should compile fftw with MPI as above.<br> <br> None of this will help if the MPI environment is not configured, e.g. a<br> hostfile set up. Chandan needs to get a test MPI program to run before<br>
there is evidence any of this discussion belongs on the GROMACS mailing<br> last.<br> <br> Mark<br> <br> <br> ------------------------------<br> <br> Message: 2<br> Date: Mon, 01 Feb 2010 22:34:06 +1100<br> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Re : MPI<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <<a href="mailto:4B66BC2E.9090109@anu.edu.au">4B66BC2E.9090109@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br> <br> On 01/02/10 21:41, bharat gupta wrote:<br> > hi all,<br> > Can anyboddy tell me from where I can get full detail of MPI with<br> > respect to GROMACS ..<br>
<br> This question is too general. Please search the GROMACS website for<br> whatever you're really searching for, and if that fails, ask a focussed<br> question.<br> <br> Mark<br> <br> <br> ------------------------------<br>
<br> Message: 3<br> Date: Mon, 01 Feb 2010 15:27:58 +0530<br> From: "011013021-Jyotsna" <<a href="mailto:011013021@bioinfo.sastra.edu">011013021@bioinfo.sastra.edu</a>><br> Subject: [gmx-users] H2 topology<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> Cc: <a href="mailto:jyots18888@gmail.com">jyots18888@gmail.com</a><br> Message-ID: <<a href="mailto:web-2479207@sastra.edu">web-2479207@sastra.edu</a>><br>
Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"<br> <br> Dear all,<br> <br> I want to run a simulation for an enzyme. It demands me to<br> incorporate a Molecular hydrogen Topology with a dummy<br>
atom in between in the simulation in order to study the<br> path of hydrogen in it.The problem is , the topology file<br> I built induces many errors when i come to the energy<br> minimization step. The version of gromacs I am using is<br>
4.0. The topology file I built is as follows<br> <br> <br> <br> [ moleculetype ]<br> ;name nrexcl<br> H2 3<br> <br> [ atoms ]<br>
; nr type
resnr residu atom cgnr<br> charge mass ; total charge<br> 1
H 1
H2 H1 1<br> 0.475 1.00800 ; 0.00<br> 2
H 1
H2 H2 1<br> 0.475 1.00800 ; 0.00<br> 3
DUM 1
H2 DUM
1<br> -0.950 0.000<br> <br> [ virtual_sites2 ]<br> ; Site from funct a<br> 3 1 2 1 0.7439756<br> <br> <br> When ever I insert the hydrogen+dummy atom topology in the<br> protein's .gro file, an error is generated regarding<br>
mismatch of residues or the dummy atom having mass 0 .<br> <br> I would be really grateful if anyone could provide me the<br> hydrogen molecule topology and give some pointers towards<br> it.<br> <br> Thank you,<br> <br>
Jyotsna<br> <br> <br> <br> ------------------------------<br> <br> Message: 4<br> Date: Mon, 01 Feb 2010 13:01:29 +0100<br> From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] H2 topology<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <<a href="mailto:4B66C299.4080301@xray.bmc.uu.se">4B66C299.4080301@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br> <br> On 2/1/10 10:57 AM, 011013021-Jyotsna wrote:<br> > Dear all,<br> ><br> > I want to run a simulation for an enzyme. It demands me to incorporate a<br>
> Molecular hydrogen Topology with a dummy atom in between in the<br> > simulation in order to study the path of hydrogen in it.The problem is ,<br> > the topology file I built induces many errors when i come to the energy<br>
> minimization step. The version of gromacs I am using is 4.0. The<br> > topology file I built is as follows<br> ><br> ><br> ><br> > [ moleculetype ]<br> > ;name nrexcl<br> > H2 3<br> ><br> > [ atoms ]<br>
> ; nr type resnr residu atom cgnr charge mass ; total charge<br> > 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00<br> > 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00<br> > 3 DUM 1 H2 DUM 1 -0.950 0.000<br> ><br> > [ virtual_sites2 ]<br>
> ; Site from funct a<br> > 3 1 2 1 0.7439756<br> ><br> ><br> > When ever I insert the hydrogen+dummy atom topology in the protein's<br> > .gro file, an error is generated regarding mismatch of residues or the<br>
> dummy atom having mass 0 .<br> ><br> > I would be really grateful if anyone could provide me the hydrogen<br> > molecule topology and give some pointers towards it.<br> ><br> <br> Please print the error message in your mail.<br>
<br> Topology look OK, but you need to add a bond or constraint.<br> Also the constant probably has to be 0.5 since you want the vsite in the<br> center of the two atoms.<br> <br> <br> > Thank you,<br> ><br> > Jyotsna<br>
><br> <br> <br> --<br> David van der Spoel, Ph.D., Professor of Biology<br> Dept. of Cell & Molec. Biol., Uppsala University.<br> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>
<br> <br> ------------------------------<br> <br> Message: 5<br> Date: Mon, 1 Feb 2010 12:16:02 +0000<br> From: Catarina Nunes <<a href="mailto:cata.nunes@gmail.com">cata.nunes@gmail.com</a>><br> Subject: [gmx-users] tutorial for ionic liquid<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> Message-ID:<br> <<a href="mailto:a3cd35831002010416r4fcbecaawbac5b4895184b87d@mail.gmail.com">a3cd35831002010416r4fcbecaawbac5b4895184b87d@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br> <br> Dear all,<br> Do you have any tutorial for ?<br> Best regards<br> Catarina<br> <br> <br> ------------------------------<br> <br> Message: 6<br> Date: Mon, 01 Feb 2010 07:18:51 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br> Subject: Re: [gmx-users] tutorial for ionic liquid<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4B66C6AB.2070503@vt.edu">4B66C6AB.2070503@vt.edu</a>><br> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br> <br> <br> <br> Catarina Nunes wrote:<br> > Dear all,<br> > Do you have any tutorial for ?<br>
> Best regards<br> > Catarina<br> <br> Gromacs tutorials can be found at:<br> <br> <a href="http://www.gromacs.org/Documentation/Tutorials">http://www.gromacs.org/Documentation/Tutorials</a><br> <br> If you don't find it there, try Google. If you don't find it there, it probably<br>
doesn't exist :)<br> <br> -Justin<br> <br> --<br> ========================================<br> <br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> MILES-IGERT Trainee<br> Department of Biochemistry<br>
Virginia Tech<br> Blacksburg, VA<br> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br> ========================================<br> <br> <br> ------------------------------<br> <br> Message: 7<br> Date: Mon, 1 Feb 2010 05:05:31 -0800 (PST)<br> From: oguz gurbulak <<a href="mailto:gurbulakoguz@yahoo.com">gurbulakoguz@yahoo.com</a>><br>
Subject: [gmx-users] non-equilibrium MD simulations<br> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> Message-ID: <<a href="mailto:547100.67241.qm@web36302.mail.mud.yahoo.com">547100.67241.qm@web36302.mail.mud.yahoo.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br> <br> Dear All,<br> <br>
I'm searching for a non-equilibrium MD tutorial done with
Gromacs. Could you please help me to find a NEMD tutorial ?<br> <br> Thank in advance .<br> <br> <br> <br> <br> <br> -------------- next part --------------<br> An HTML attachment was scrubbed...<br> URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100201/ff079c22/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100201/ff079c22/attachment-0001.html</a><br>
<br> ------------------------------<br> <br> Message: 8<br> Date: Mon, 01 Feb 2010 08:08:02 -0500<br> From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br> Subject: Re: [gmx-users] non-equilibrium MD simulations<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <<a href="mailto:4B66D232.3020307@vt.edu">4B66D232.3020307@vt.edu</a>><br> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br> <br> <br> oguz gurbulak wrote:<br> > Dear All,<br> ><br> > I'm searching for a non-equilibrium MD tutorial done with Gromacs.<br> > Could you please help me to find a NEMD tutorial ?<br> ><br> <br>
"Non-equilibrium" can encompass a variety of topics, so if you want specific<br> advice, you'll have to be more specific. And, as I just mentioned to someone else:<br> <br> <a href="http://lists.gromacs.org/pipermail/gmx-users/2010-February/048498.html">http://lists.gromacs.org/pipermail/gmx-users/2010-February/048498.html</a><br>
<br> -Justin<br> <br> > Thank in advance .<br> ><br> ><br> ><br> ><br> <br> --<br> ========================================<br> <br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> MILES-IGERT Trainee<br>
Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br> <br> End of gmx-users Digest, Vol 70, Issue 5<br> ****************************************<br> </blockquote>
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