[gmx-users] Re: gmx-users Digest, Vol 84, Issue 28

Mon Apr 4 23:43:00 CEST 2011

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-request at gromacs.org>

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> 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 <rifaximina at gmail.com>
> Subject: [gmx-users] how to Installing GROMACS in rocks cluster
> To: gmx-users at gromacs.org
> Message-ID: <BANLkTimh_Lx_E9B=fJ-WRypK-vh=cF2xQQ at 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
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> ------------------------------
>
> Message: 2
> Date: Mon, 4 Apr 2011 14:11:48 -0400
> From: shivangi nangia <shivangi.nangia at gmail.com>
> Subject: [gmx-users] autocorrelation functions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTi=HS9T7zpWkhEVFsYmZjrV=he1RZA at 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
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> ------------------------------
>
> Message: 3
> Date: Mon, 4 Apr 2011 20:36:37 +0200
> From: Luca Bellucci <lcbllcc at gmail.com>
> Subject: Re: [gmx-users] FEP and loss of performance
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <201104042036.37450.lcbllcc at 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 <ssham44 at yahoo.com>
> Subject: [gmx-users] g_chi
> To: gmx-users at gromacs.org
> Message-ID: <146698.42935.qm at 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
>
>
>
>
>
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> ------------------------------
>
> Message: 5
> Date: Mon, 04 Apr 2011 22:31:17 +0200
> From: Francesco Oteri <francesco.oteri at gmail.com>
> Subject: Re: [gmx-users] g_chi
> To: gmx-users at gromacs.org
> Message-ID: <4D9A2A95.9010400 at 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
> >
> >
> >
> >
> >
>
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> ------------------------------
>
> Message: 6
> Date: Mon, 04 Apr 2011 16:43:29 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] g_chi
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D9A2D71.60001 at 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
>
> ========================================
>
>
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> End of gmx-users Digest, Vol 84, Issue 28
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