Dear colleagues.<br><br>I would like to share with the community this. Searching I can find this:<br><br><a href="http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/">http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/</a><br>
<h1 style="width: 530px;">Compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0</h1>I think is very useful for People who have the same objective. However, in one section the tutorial refers that the GROMACS version 4.5.3 had some bugs. I would like to install version GROMACS 4.5.4, Does somebody know if this version has the same problems?<br>
<br>Thanks in advance.<br><br>Miguel Quiliano.<br><br> <br><br><div class="gmail_quote">2011/4/4 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. how to Installing GROMACS in rocks cluster (Miguel Quiliano Meza)<br>
2. autocorrelation functions (shivangi nangia)<br>
3. Re: FEP and loss of performance (Luca Bellucci)<br>
4. g_chi (simon sham)<br>
5. Re: g_chi (Francesco Oteri)<br>
6. Re: g_chi (Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 4 Apr 2011 13:58:40 -0400<br>
From: Miguel Quiliano Meza <<a href="mailto:rifaximina@gmail.com">rifaximina@gmail.com</a>><br>
Subject: [gmx-users] how to Installing GROMACS in rocks cluster<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <BANLkTimh_Lx_E9B=fJ-WRypK-vh=<a href="mailto:cF2xQQ@mail.gmail.com">cF2xQQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Colleagues.<br>
<br>
I have been searching information about "HOW TO INSTALL GROMACS in rocks<br>
cluster?". Unfortunately, the information that I found is not clear.<br>
<br>
Someone can help me with this question. Maybe there are basic but important<br>
steps that I have to keep in mind. Could you please share yours experiences?<br>
<br>
<br>
Thank you in advance.<br>
<br>
Miguel Quiliano.<br>
<br>
P.D I have installed rocks cluster 5.4<br>
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Message: 2<br>
Date: Mon, 4 Apr 2011 14:11:48 -0400<br>
From: shivangi nangia <<a href="mailto:shivangi.nangia@gmail.com">shivangi.nangia@gmail.com</a>><br>
Subject: [gmx-users] autocorrelation functions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTi=HS9T7zpWkhEVFsYmZjrV=<a href="mailto:he1RZA@mail.gmail.com">he1RZA@mail.gmail.com</a>><br>
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<br>
Hello all,<br>
<br>
<br>
I need to calculate the end-to-end vector autocorrelation function of my<br>
polymer chains. I could get the velocity autocorrelation function using<br>
g_velacc tool.<br>
<br>
Is there a tool available for calculating end-to-end vector autocorrelation<br>
function? If not, then is there an easy way to modify/morph the g_velacc.c<br>
program to do other autocorrelation function calculations?<br>
<br>
<br>
Thanks,<br>
Shivangi<br>
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Message: 3<br>
Date: Mon, 4 Apr 2011 20:36:37 +0200<br>
From: Luca Bellucci <<a href="mailto:lcbllcc@gmail.com">lcbllcc@gmail.com</a>><br>
Subject: Re: [gmx-users] FEP and loss of performance<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:201104042036.37450.lcbllcc@gmail.com">201104042036.37450.lcbllcc@gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Yes i am testing the possibility to perform an Hamiltonian-REMD<br>
Energy barriers can be overcome increasing the temperature system or scaling<br>
potential energy with a lambda value, these methods are "equivalent".<br>
Both have advantages and disavantages, at this stage it is not the right place<br>
to debate on it. The main problem seems to be how to overcome to the the loss<br>
of gromacs performance in such calculation. At this moment it seems an<br>
intrinsic code problem.<br>
Is it possible?<br>
<br>
> >> Dear Chris and Justin<br>
> >><br>
> >>/ Thank you for your precious suggestions<br>
><br>
> />>/ This is a test that i perform in a single machine with 8 cores<br>
> />>/ and gromacs 4.5.4.<br>
> />>/<br>
> />>/ I am trying to enhance the sampling of a protein using the<br>
> decoupling scheme />>/ of the free energy module of gromacs. However when<br>
> i decouple only the />>/ protein, the protein collapsed. Because i<br>
> simulated in NVT i thought that />>/ this was an effect of the solvent. I<br>
> was trying to decouple also the solvent />>/ to understand the system<br>
> behavior.<br>
> />>/<br>
> /><br>
><br>
> >Rather than suspect that the solvent is the problem, it's more likely that<br>
> >decoupling an entire protein simply isn't stable. I have never tried<br>
> > anything that enormous, but the volume change in the system could be<br>
> > unstable, along with any number of factors, depending on how you approach<br>
> > it.<br>
> ><br>
> >If you're looking for better sampling, REMD is a much more robust approach<br>
> > than trying to manipulate the interactions of huge parts of your system<br>
> > using the free energy code.<br>
><br>
> Presumably Luca is interested in some type of hamiltonian exchange where<br>
> lambda represents the interactions between the protein and the solvent?<br>
> This can actually be a useful method for enhancing sampling. I think it's<br>
> dangerous if we rely to heavily on "try something else". I still see no<br>
> methodological reason a priori why there should be any actual slowdown, so<br>
> that makes me think that it's an implementation thing, and there is at<br>
> least the possibility that this is something that could be fixed as an<br>
> enhancement.<br>
><br>
> Chris.<br>
><br>
><br>
> -Justin<br>
><br>
> >/ I expected a loss of performance, but not so drastic.<br>
><br>
> />/ Luca<br>
> />/<br>
> />>/ Load balancing problems I can understand, but why would it take<br>
> longer />>/ in absolute time? I would have thought that some nodes would<br>
> simple be />>/ sitting idle, but this should not cause an increase in the<br>
> overall />>/ simulation time (15x at that!).<br>
> />>/<br>
> />>/ There must be some extra communication?<br>
> />>/<br>
> />>/ I agree with Justin that this seems like a strange thing to do, but<br>
> />>/ still I think that there must be some underlying coding issue<br>
> (probably />>/ one that only exists because of a reasonable assumption<br>
> that nobody />>/ would annihilate the largest part of their system).<br>
> />>/<br>
> />>/ Chris.<br>
> />>/<br>
> />>/ Luca Bellucci wrote:<br>
> />>>/ / Hi Chris,<br>
> />>/ />/ thank for the suggestions,<br>
> />>/ />/ in the previous mail there is a mistake because<br>
> />>/ />/ couple-moltype = SOL (for solvent) and not "Protein_chaim_P".<br>
> />>/ />/ Now the problem of the load balance seems reasonable, because<br>
> />>/ />/ the water box is large ~9.0 nm.<br>
> />>/ /<br>
> />>/ Now your outcome makes a lot more sense. You're decoupling all of<br>
> the />>/ solvent? I don't see how that is going to be physically stable or<br>
> terribly /<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Mon, 4 Apr 2011 13:19:27 -0700 (PDT)<br>
From: simon sham <<a href="mailto:ssham44@yahoo.com">ssham44@yahoo.com</a>><br>
Subject: [gmx-users] g_chi<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:146698.42935.qm@web36702.mail.mud.yahoo.com">146698.42935.qm@web36702.mail.mud.yahoo.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi,<br>
I have 2 questions on using g_chi to calculate only one omega angle for X-Pro.<br>
<br>
1. I used the following command:<br>
<br>
"g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg" and got the following message:<br>
Fatal error:<br>
Library file in current dir nor not found aminoacids.datin default directories.<br>
(You can set the directories to search with the GMXLIB path variable)<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a>"<br>
<br>
2. The command does not allow using index file. How can I calculate just one dihedral angle?<br>
<br>
Thanks for your help in advance.<br>
<br>
Simon Sham<br>
<br>
<br>
<br>
<br>
<br>
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Message: 5<br>
Date: Mon, 04 Apr 2011 22:31:17 +0200<br>
From: Francesco Oteri <<a href="mailto:francesco.oteri@gmail.com">francesco.oteri@gmail.com</a>><br>
Subject: Re: [gmx-users] g_chi<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:4D9A2A95.9010400@gmail.com">4D9A2A95.9010400@gmail.com</a>><br>
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<br>
Hi Simon,<br>
Regarding the first question you should set GMXLIB as $GMXDATA/gromacs/top.<br>
<br>
I don't know how to solve the second problem bacause I never used g_chi<br>
<br>
Il 04/04/2011 22:19, simon sham ha scritto:<br>
> Hi,<br>
> I have 2 questions on using g_chi to calculate only one omega angle<br>
> for X-Pro.<br>
><br>
> 1. I used the following command:<br>
><br>
> "g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg" and got the<br>
> following message:<br>
> Fatal error:<br>
> Library file in current dir nor not found aminoacids.datin default<br>
> directories.<br>
> (You can set the directories to search with the GMXLIB path variable)<br>
> For more information and tips for troubleshooting, please check the<br>
> GROMACS<br>
> website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a>"<br>
><br>
> 2. The command does not allow using index file. How can I calculate<br>
> just one dihedral angle?<br>
><br>
> Thanks for your help in advance.<br>
><br>
> Simon Sham<br>
><br>
><br>
><br>
><br>
><br>
<br>
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<br>
Message: 6<br>
Date: Mon, 04 Apr 2011 16:43:29 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] g_chi<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:4D9A2D71.60001@vt.edu">4D9A2D71.60001@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
simon sham wrote:<br>
> Hi,<br>
> I have 2 questions on using g_chi to calculate only one omega angle for<br>
> X-Pro.<br>
><br>
> 1. I used the following command:<br>
><br>
> "g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg" and got the following<br>
> message:<br>
> Fatal error:<br>
> Library file in current dir nor not found aminoacids.datin default<br>
> directories.<br>
> (You can set the directories to search with the GMXLIB path variable)<br>
> For more information and tips for troubleshooting, please check the GROMACS<br>
> website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a>"<br>
><br>
<br>
Upgrade to a newer version of Gromacs. This bug has been fixed.<br>
<br>
> 2. The command does not allow using index file. How can I calculate just<br>
> one dihedral angle?<br>
><br>
<br>
Not sure on this one, but once you have a properly-functioning executable, you<br>
should be able to tell from the output files (of which there is a .log file that<br>
should contain everything).<br>
<br>
-Justin<br>
<br>
> Thanks for your help in advance.<br>
><br>
> Simon Sham<br>
><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" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
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