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

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 4 23:47:08 CEST 2011



Miguel Quiliano Meza wrote:
> 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 v1.0
> 
> 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?
> 

It was fixed for 4.5.4.

-Justin

> Thanks in advance.
> 
> Miguel Quiliano.
> 
>  
> 
> 2011/4/4 <gmx-users-request at gromacs.org 
> <mailto: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
>     <mailto:rifaximina at gmail.com>>
>     Subject: [gmx-users] how to Installing GROMACS in rocks cluster
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Message-ID: <BANLkTimh_Lx_E9B=fJ-WRypK-vh=cF2xQQ at mail.gmail.com
>     <mailto: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
>     <mailto:shivangi.nangia at gmail.com>>
>     Subject: [gmx-users] autocorrelation functions
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <BANLkTi=HS9T7zpWkhEVFsYmZjrV=he1RZA at mail.gmail.com
>     <mailto: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 <mailto:lcbllcc at gmail.com>>
>     Subject: Re: [gmx-users] FEP and loss of performance
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <201104042036.37450.lcbllcc at gmail.com
>     <mailto: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 <mailto:ssham44 at yahoo.com>>
>     Subject: [gmx-users] g_chi
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Message-ID: <146698.42935.qm at web36702.mail.mud.yahoo.com
>     <mailto: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
>     <mailto:francesco.oteri at gmail.com>>
>     Subject: Re: [gmx-users] g_chi
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Message-ID: <4D9A2A95.9010400 at gmail.com
>     <mailto: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 <mailto:jalemkul at vt.edu>>
>     Subject: Re: [gmx-users] g_chi
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <4D9A2D71.60001 at vt.edu <mailto: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 <http://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
>     *****************************************
> 
> 

-- 
========================================

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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