[gmx-users] gromacs.org_gmx-users Digest, Vol 134, Issue 45

Tue Jun 9 08:38:01 CEST 2015

Hi everyone

I'm going to run md simulation but when i use grompp command i face this
warning:

 WARNING 1 [file "DRGGMX.ITP", line 18]:
>    Too few parameters on line (source file toppush.c, line 731)

can everyone help me please?

On Mon, Jun 8, 2015 at 2:18 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Re: Problems installing gromacs 5.0.4 with plumed 2.1.2   for
>       MPI (jkrieger at mrc-lmb.cam.ac.uk)
>    2. Re: Microwave (Mostafa Javaheri)
>    3. gmx distance (Poncho Arvayo Zatarain)
>    4. cudaStreamSynchronize failed in cu_blockwait_nb (Alex)
>    5. Re: cudaStreamSynchronize failed in cu_blockwait_nb (Alex)
>    6. Immediate PhD Opening In Computational Structural Biology Of
>       Membrane Proteins (Marawan Hussien)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 8 Jun 2015 18:57:37 +0100
> From: jkrieger at mrc-lmb.cam.ac.uk
> To: "James Krieger" <jkrieger at mrc-lmb.cam.ac.uk>
> Cc: gmx users-list <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed
>         2.1.2   for MPI
> Message-ID:
>         <f747d8a83bda90990801c5edbe619a2c.squirrel at mail.mrc-lmb.cam.ac.uk>
> Content-Type: text/plain
>
> More details are available on the plumed forum google group at
>
> https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ
>
> > Hi,
> >
> > I have successfully installed plumed-2.1.2 (I believe with MPI
> > capabilities) and patched it onto gromacs-5.0.4, I am now trying to
> > install the gromacs and it's not working. Here are my errors from make:
> >
> > collect2: error: ld returned 1 exit status
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for target
> > 'lib/libgromacs_mpi.so.0.0.0' failed
> > make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1
> > CMakeFiles/Makefile2:1948: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:146: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > I have successfully installed the latest gcc compilers and tried to tell
> > gromacs to use them with the following command (not sure if this is
> > right):
> > ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON
> > -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc
> >
> > In any case I get similar errors using the default compilers on my
> system.
> >
> > I am installing on a front-end node of our cluster at the LMB, which has
> a
> > shared filesystem.
> >
> > Please let me know if there's anything else I need to tell you so that
> you
> > can help.
> >
> > Many thanks
> > James
> >
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 8 Jun 2015 22:34:02 +0430
> From: Mostafa Javaheri <javaheri.gromacs at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Microwave
> Message-ID:
>         <CAH0JJJKJdmfYA=Yvt=
> JdSENAiUwdTweeXrAU0LZ2dndjtKRgRw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Mark,
>
> The authors didn't circulate the modified version of GROMACS and they
> couldn't be able for any help. It would be very kind of you if you could
> give me some information about which file or files of the source code
> should I alter for achieving this purpose.
>
> Best,
>
> Mostafa
>
> On Mon, Jun 8, 2015 at 8:05 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You'd have to contact the authors to get their modified version.
> >
> > Mark
> >
> > On Sun, Jun 7, 2015 at 11:09 PM Mostafa Javaheri <
> > javaheri.gromacs at gmail.com>
> > wrote:
> >
> > > Hi all,
> > >
> > > Thanks for your replies,
> > >
> > > I searched about the simulation under e/m field and as far as I
> > understood,
> > > I have to alter the source code for that, but I don't know how to do
> this
> > > and which part of the source code must change exactly. several studies
> > have
> > > been performed by Niall J. English and co (
> > >
> http://scitation.aip.org/content/aip/journal/jcp/131/3/10.1063/1.3184794
> > )
> > > and (http://adsabs.harvard.edu/abs/2003JChPh.118.1589E) which I'm
> > tending
> > > to do the same but with different protein, due to the correspondence,
> > they
> > > used modified version of GROMACS 3 in their studies.
> > > I would be thankful if you could give me some idea about this kind of
> > > modification?
> > >
> > > Best,
> > >
> > > Mostafa
> > >
> > > On Tue, Jun 2, 2015 at 4:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > > >
> > > >
> > > > On 6/2/15 4:31 AM, Mostafa Javaheri wrote:
> > > >
> > > >> Dear Justin,
> > > >>
> > > >> How could I simulate a membrane protein while there is microwave
> > > >> radiations in
> > > >> one direction e.g. in direction of z-axis? Should I change the
> > > >> delta-lambda
> > > >>
> > > >
> > > > delta-lambda is a free energy option.
> > > >
> > > >  or Is this accessible via electric field option? If I have to use
> > > electric
> > > >> field option, should I patch the mdrun (
> > > >>
> > http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun
> > > )?
> > > >>
> > > >>
> > > > Electric fields are already supported, but I don't think this is
> > > > physically what you want.  I have no idea how to microwave an MD
> > > simulation.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==================================================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > >
> > > > Department of Pharmaceutical Sciences
> > > > School of Pharmacy
> > > > Health Sciences Facility II, Room 629
> > > > University of Maryland, Baltimore
> > > > 20 Penn St.
> > > > Baltimore, MD 21201
> > > >
> > > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > > http://mackerell.umaryland.edu/~jalemkul
> > > >
> > > > ==================================================
> > > > --
> > > > Gromacs Users mailing list
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 8 Jun 2015 15:35:47 -0300
> From: Poncho Arvayo Zatarain <poncho_8629 at hotmail.com>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] gmx distance
> Message-ID: <SNT150-W36E14467980DEAFB2B942180BF0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Helecho "3 4"| g_distlo, i want to introduce a coomand in Gromacs 5.0.4
> with the initial echo "3 4"| g_dist. Should i use gmx distance echo "3 4"|
> g_dist and the rest of the commnand? This is the complete command i want to
> use  echo "3 4"| g_dist -f dppc128_1-nj-ct-nobox.xtc -s dppc128_1.tpr -o
> dppc128-Dpp.xvg -n Dpp.ndx -b 20000. Or how should i use that command on
> gromacs 5.0.4? Because i read the g_dist in gromacs 5.0 has been modified.
> Thanks
>
> ------------------------------
>
> Message: 4
> Date: Mon, 8 Jun 2015 14:07:27 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] cudaStreamSynchronize failed in cu_blockwait_nb
> Message-ID:
>         <CAMJZ6qEE6DdbN7vf4N7WhdMh1=usB-WbFWY-acFfDhfg=-
> oJVg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all,
>
> I am running a GPU-accelerated test (GMX 5.0.5) and, after about 60K steps
> of what seems to be a huge speed-up, I get the error from the subject with
> the following comment: "unspecified launch failure."
>
> This is on an 8-core (16-thread) Intel CPU and two Tesla cards. The run
> command is:
>
> mdrun -ntomp 4 <file directives>
>
> I saw some previous messages on this error, but not sure there's a
> solution.
> Any thoughts? I will provide any additional info as needed. If there are
> additional options necessary to debug etc, could you provide the exact
> command line?
>
> Thanks,
>
> Alex
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 8 Jun 2015 14:25:03 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] cudaStreamSynchronize failed in
>         cu_blockwait_nb
> Message-ID:
>         <CAMJZ6qEs9_8-Jq8m6FovmZB6siiKR3UAZxY=
> 2VUjVQnVdzCkfw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Additional info:
>
> The base system is a SuperMicro X8DTG-D motherboard with dual Xeon E5620
> CPUs at 2.4 GHz, and 24 GB of DDR3 ECC RAM
>
> The GPUs are two NVidia Tesla C2075s
>
> Running under Ubuntu 14.04 LTS 64-bit, kernel 3.13.0-53, with CUDA 7.0,
> installed via the NVIDIA-provided .deb file,
> cuda-repo-ubuntu1404-7-0-local_7.0-28_amd64.deb, followed by the usual
> apt-get update/upgrade.
>
> Nvcc reports version 7.0.27.
>
> GMX version is 5.0.5, locally built, with auto-detected options, including
> "GMX_GPU ON", and "GMX_SIMD SSE4.1"
>
> On Mon, Jun 8, 2015 at 2:07 PM, Alex <nedomacho at gmail.com> wrote:
>
> > Hi all,
> >
> > I am running a GPU-accelerated test (GMX 5.0.5) and, after about 60K
> steps
> > of what seems to be a huge speed-up, I get the error from the subject
> with
> > the following comment: "unspecified launch failure."
> >
> > This is on an 8-core (16-thread) Intel CPU and two Tesla cards. The run
> > command is:
> >
> > mdrun -ntomp 4 <file directives>
> >
> > I saw some previous messages on this error, but not sure there's a
> > solution.
> > Any thoughts? I will provide any additional info as needed. If there are
> > additional options necessary to debug etc, could you provide the exact
> > command line?
> >
> > Thanks,
> >
> > Alex
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 8 Jun 2015 21:18:08 +0000 (UTC)
> From: Marawan Hussien <marawanhussain at yahoo.com>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Immediate PhD Opening In Computational Structural
>         Biology Of Membrane Proteins
> Message-ID:
>         <2008956357.9076129.1433798288099.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Immediate PhD Opening In Dr. Khaled Barakat?s Lab, Faculty OfPharmacy,
> University Of Alberta.
>
> ?
>
> Specialization:?Computational Structural Biology Of MembraneProteins
>
> ?
>
> Term:?4 Years Fully Funded PhD Studentship
>
> ?
>
> A four years fully funded PhD studentship is available immediatelyin the
> computational chemistry and drug discovery lab of Dr. Khaled Barakat atthe
> Faculty of Pharmacy, University of Alberta, Canada.?Successfulapplicants
> will employ state-of-the-art computational techniques and highperformance
> computing facilities accessible to the lab to work on thestructural biology
> of membrane proteins.
>
>
> ?
> Applicants should have good undergraduate record in a research
> richenvironment. They should also have strong communication skills, and an
> abilityto collaborate effectively.
>
>
> ?
> The following qualifications are essential:
>
>
> ?
> 1.????????????M.Sc. degree (or equivalenteg: first class honor) in
> chemistry, physics, or a related discipline (completedor near completion)
> as well as outstanding B.Sc. graduates (with a 3.5/4.0 orhigher GPA).
>
> 2.????????????Strong aptitudes and in depthpassion in physical chemistry
> and in mathematics.
>
> 3.????????????Interest in biochemistry,physiology, computer simulations.
>
> 4.????????????Familiarity with UNIX/Linuxoperating systems and python
> scripting.
>
> 5.????????????At least one first authorpublication in a closely related
> field.
>
> 6.????????????Familiarity withcomputational structural
> biology/bioinformatics techniques, such as homologymodeling, classical MD
> simulation, docking, etc.
>
> 7.????????????Experience with at least oneof the software packages for
> atomistic biological simulations, such as AMBER,NAMD, GROMACS is
> recommended.
>
>
> Initial appointment will be for four years; this can be increased up to 5
> yearsdepending on the availability of funding.
>
>
> To apply for this position, please send your most updated CV and a
> briefstatement of research interests, along with the names and contact
> informationof at least two referees, to:?Dr. Khaled Barakat (email:?
> kbarakat at ualberta.ca)
>
>
> ?
>
> ?
>
> ?
>
> ?
>
>
> ------------------------------
>
> --
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> End of gromacs.org_gmx-users Digest, Vol 134, Issue 45
> ******************************************************
>