Dear colleagues. I would like to share with the community this. Searching I can find this:
http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/ Compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0I 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? Thanks in advance. Miguel Quiliano. 2011/4/4 <gmx-users-requ...@gromacs.org> > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > 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 > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. how to Installing GROMACS in rocks cluster (Miguel Quiliano Meza) > 2. autocorrelation functions (shivangi nangia) > 3. Re: FEP and loss of performance (Luca Bellucci) > 4. g_chi (simon sham) > 5. Re: g_chi (Francesco Oteri) > 6. Re: g_chi (Justin A. Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 4 Apr 2011 13:58:40 -0400 > From: Miguel Quiliano Meza <rifaxim...@gmail.com> > Subject: [gmx-users] how to Installing GROMACS in rocks cluster > To: gmx-users@gromacs.org > Message-ID: <BANLkTimh_Lx_E9B=fJ-WRypK-vh=cf2...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Colleagues. > > I have been searching information about "HOW TO INSTALL GROMACS in rocks > cluster?". Unfortunately, the information that I found is not clear. > > Someone can help me with this question. Maybe there are basic but important > steps that I have to keep in mind. Could you please share yours > experiences? > > > Thank you in advance. > > Miguel Quiliano. > > P.D I have installed rocks cluster 5.4 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/ef4b39fe/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 4 Apr 2011 14:11:48 -0400 > From: shivangi nangia <shivangi.nan...@gmail.com> > Subject: [gmx-users] autocorrelation functions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <BANLkTi=HS9T7zpWkhEVFsYmZjrV=he1...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > > I need to calculate the end-to-end vector autocorrelation function of my > polymer chains. I could get the velocity autocorrelation function using > g_velacc tool. > > Is there a tool available for calculating end-to-end vector autocorrelation > function? If not, then is there an easy way to modify/morph the g_velacc.c > program to do other autocorrelation function calculations? > > > Thanks, > Shivangi > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/cb2a4e0a/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Mon, 4 Apr 2011 20:36:37 +0200 > From: Luca Bellucci <lcbl...@gmail.com> > Subject: Re: [gmx-users] FEP and loss of performance > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <201104042036.37450.lcbl...@gmail.com> > Content-Type: text/plain; charset="utf-8" > > Yes i am testing the possibility to perform an Hamiltonian-REMD > Energy barriers can be overcome increasing the temperature system or > scaling > potential energy with a lambda value, these methods are "equivalent". > Both have advantages and disavantages, at this stage it is not the right > place > to debate on it. The main problem seems to be how to overcome to the the > loss > of gromacs performance in such calculation. At this moment it seems an > intrinsic code problem. > Is it possible? > > > >> Dear Chris and Justin > > >> > > >>/ Thank you for your precious suggestions > > > > />>/ This is a test that i perform in a single machine with 8 cores > > />>/ and gromacs 4.5.4. > > />>/ > > />>/ I am trying to enhance the sampling of a protein using the > > decoupling scheme />>/ of the free energy module of gromacs. However > when > > i decouple only the />>/ protein, the protein collapsed. Because i > > simulated in NVT i thought that />>/ this was an effect of the solvent. > I > > was trying to decouple also the solvent />>/ to understand the system > > behavior. > > />>/ > > /> > > > > >Rather than suspect that the solvent is the problem, it's more likely > that > > >decoupling an entire protein simply isn't stable. I have never tried > > > anything that enormous, but the volume change in the system could be > > > unstable, along with any number of factors, depending on how you > approach > > > it. > > > > > >If you're looking for better sampling, REMD is a much more robust > approach > > > than trying to manipulate the interactions of huge parts of your system > > > using the free energy code. > > > > Presumably Luca is interested in some type of hamiltonian exchange where > > lambda represents the interactions between the protein and the solvent? > > This can actually be a useful method for enhancing sampling. I think it's > > dangerous if we rely to heavily on "try something else". I still see no > > methodological reason a priori why there should be any actual slowdown, > so > > that makes me think that it's an implementation thing, and there is at > > least the possibility that this is something that could be fixed as an > > enhancement. > > > > Chris. > > > > > > -Justin > > > > >/ I expected a loss of performance, but not so drastic. > > > > />/ Luca > > />/ > > />>/ Load balancing problems I can understand, but why would it take > > longer />>/ in absolute time? I would have thought that some nodes would > > simple be />>/ sitting idle, but this should not cause an increase in > the > > overall />>/ simulation time (15x at that!). > > />>/ > > />>/ There must be some extra communication? > > />>/ > > />>/ I agree with Justin that this seems like a strange thing to do, but > > />>/ still I think that there must be some underlying coding issue > > (probably />>/ one that only exists because of a reasonable assumption > > that nobody />>/ would annihilate the largest part of their system). > > />>/ > > />>/ Chris. > > />>/ > > />>/ Luca Bellucci wrote: > > />>>/ / Hi Chris, > > />>/ />/ thank for the suggestions, > > />>/ />/ in the previous mail there is a mistake because > > />>/ />/ couple-moltype = SOL (for solvent) and not "Protein_chaim_P". > > />>/ />/ Now the problem of the load balance seems reasonable, because > > />>/ />/ the water box is large ~9.0 nm. > > />>/ / > > />>/ Now your outcome makes a lot more sense. You're decoupling all of > > the />>/ solvent? I don't see how that is going to be physically stable > or > > terribly / > > > > > ------------------------------ > > Message: 4 > Date: Mon, 4 Apr 2011 13:19:27 -0700 (PDT) > From: simon sham <ssha...@yahoo.com> > Subject: [gmx-users] g_chi > To: gmx-users@gromacs.org > Message-ID: <146698.42935...@web36702.mail.mud.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > I have 2 questions on using g_chi to calculate only one omega angle for > X-Pro. > > 1. I used the following command: > > "g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg" and got the following > message: > Fatal error: > Library file in current dir nor not found aminoacids.datin default > directories. > (You can set the directories to search with the GMXLIB path variable) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors"; > > 2. The command does not allow using index file. How can I calculate just > one dihedral angle? > > Thanks for your help in advance. > > Simon Sham > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/3bf67b43/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 04 Apr 2011 22:31:17 +0200 > From: Francesco Oteri <francesco.ot...@gmail.com> > Subject: Re: [gmx-users] g_chi > To: gmx-users@gromacs.org > Message-ID: <4d9a2a95.9010...@gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Simon, > Regarding the first question you should set GMXLIB as $GMXDATA/gromacs/top. > > I don't know how to solve the second problem bacause I never used g_chi > > Il 04/04/2011 22:19, simon sham ha scritto: > > Hi, > > I have 2 questions on using g_chi to calculate only one omega angle > > for X-Pro. > > > > 1. I used the following command: > > > > "g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg" and got the > > following message: > > Fatal error: > > Library file in current dir nor not found aminoacids.datin default > > directories. > > (You can set the directories to search with the GMXLIB path variable) > > For more information and tips for troubleshooting, please check the > > GROMACS > > website at http://www.gromacs.org/Documentation/Errors"; > > > > 2. The command does not allow using index file. How can I calculate > > just one dihedral angle? > > > > Thanks for your help in advance. > > > > Simon Sham > > > > > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/df0ca069/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Mon, 04 Apr 2011 16:43:29 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] g_chi > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4d9a2d71.60...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > simon sham wrote: > > Hi, > > I have 2 questions on using g_chi to calculate only one omega angle for > > X-Pro. > > > > 1. I used the following command: > > > > "g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg" and got the following > > message: > > Fatal error: > > Library file in current dir nor not found aminoacids.datin default > > directories. > > (You can set the directories to search with the GMXLIB path variable) > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors"; > > > > Upgrade to a newer version of Gromacs. This bug has been fixed. > > > 2. The command does not allow using index file. How can I calculate just > > one dihedral angle? > > > > Not sure on this one, but once you have a properly-functioning executable, > you > should be able to tell from the output files (of which there is a .log file > that > should contain everything). > > -Justin > > > Thanks for your help in advance. > > > > Simon Sham > > > > > > > > > > > > -- > ======================================== > > 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@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 84, Issue 28 > ***************************************** >
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