[gmx-users] gromacs.org_gmx-users Digest, Vol 161, Issue 20

Thu Sep 7 22:10:05 CEST 2017

I have used below mdrun command

taskset -c 0-79 gmx mdrun -deffnm md_0_1 -v

i am not sure whether i have to apply mpi threads.

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On Fri, Sep 8, 2017 at 1:22 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Re: Incorrect link for release notes of gromacs 2016.3
>       (Szil?rd P?ll)
>    2. Diffusion coefficient (Sohaib. Mohammed)
>    3. Re: Merging different topology files (Justin Lemkul)
>    4. Re: purpose of step pdb files during MD (Justin Lemkul)
>    5. gromacs installation (vijayakumar gosu)
>    6. Re: gromacs installation (Wes Barnett)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 7 Sep 2017 18:59:24 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Incorrect link for release notes of gromacs
>         2016.3
> Message-ID:
>         <CANnYEw4jCoCBu1Q35gm7oGKvWTEdD6EAfjb8GETi9B+MUeOQPw at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Fixed it, thanks ?ke!
> --
> Szil?rd
>
>
> On Thu, Sep 7, 2017 at 6:36 PM, ?ke Sandgren <ake.sandgren at hpc2n.umu.se>
> wrote:
> > Hi!
> >
> > The link for the release notes of gromacs 2016.3 on www.gromacs.org is
> > pointing to 2016.1
> >
> > --
> > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> > Internet: ake at hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
> > Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>
> ------------------------------
>
> Message: 2
> Date: Thu, 7 Sep 2017 14:07:57 -0500
> From: "Sohaib. Mohammed" <sohaibmohammed10 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Diffusion coefficient
> Message-ID:
>         <CAJs3nOocAkO2-VpuQi_t3+U52DC9wcwkGjxrtr9kYCGWOBXXQQ@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hey Users,
>
> I want to calculate the diffusion coefficient using gmx msd. I want to
> divide the box into slices of 5 A parallel to z axis and calculate the
> diffusion coefficient for each slice. My question is how to make these
> slices, I've tried gmx trajconv but didn't work with me. I believe it's
> quite simple and provided by gromacs, but I am struggling with it.
> Appreciate any idea on how to make these slices.
>
> Thank you,
> Sohaib
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 7 Sep 2017 15:08:49 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Merging different topology files
> Message-ID: <2b8ad61e-73e4-75fe-7e1f-195376985af9 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 9/7/17 10:19 AM, Momin Ahmad wrote:
> > Hello all,
> >
> > is there a simple way to merge two or more topology files into one? I
> > am trying to use grompp to set up a simulation but my solvation
> > contains different molecules which have different .top files. I also
> > tried creating a main topology file which includes the other two
> > topologies but without success. Hope anyone knows how to solve this.
> >
>
> The #include mechanism is the only way to do this.? If you have two .top
> (system topology) files, then:
>
> 1. Remove any #include statement for a parent force field (i.e. the file
> with [defaults] in it)
> 2. Remove any [system] or [molecules] directive
>
> (you now have proper .itp format)
>
> 3. Remove any redundant #include statements (e.g. for water, ions) to
> avoid "moleculetype redefined" errors
> 4. Construct a new .top that #includes a parent force field, your two
> new .itp files, and has [system] and [molecules] directives.
>
> -Justin
>
> --
>
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 7 Sep 2017 15:10:00 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] purpose of step pdb files during MD
> Message-ID: <c3ba28ac-7dfd-4143-f749-1171850b5336 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 9/7/17 10:29 AM, Vedat Durmaz wrote:
> > i really appreciate this pretty informative answer. and do you also
> know, what the infix "n254" or "n2" stands for?
>
> Node ID.
>
> > what i found strange is that the error occurs after nearly 10M MD steps.
> in other copies of the same system, the error doesn't occur at all even
> after the entire predefines time span (40ns).
> >
> > it's a long fibril chain (>200 repeating units) of a 7mer polypeptide.
> the walls of the triclinic simulation box of size 10x8x70 nm have an
> initial distance of 1.5 nm to the fibril and i have chosen "comm-mode  =
> linear" in order to keep the system centered. i'm actually wondering,
> whether that might have caused the error or whether the system will for
> sure crash if the long chain changes its shape to some spheric one that
> doesn't fit the slim box anymore.
> >
> > do you have any experience with that?
>
> Nope, sorry.? A crash after a long simulation time is very unusual and
> hard to diagnose.? Normally things fail rather quickly.? Does your
> GROMACS installation pass all regression tests?
>
> -Justin
>
> --
>
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 8 Sep 2017 04:25:48 +0900
> From: vijayakumar gosu <vijayakumargosu at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] gromacs installation
> Message-ID:
>         <CAB_TNdTcZv3ckSjiW5QQNj2W5rMRhvpCma2jJdhu2k+nsnyd4w at mail.gmail.
> com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus.
> I am allotted to use only 2 nodes with 80 cpus. after installation when i
> did sample md run only 20 cpus are being utilized. How can I fully utilize
> the all 80 CPUs for mdrun.
>
> I have used below cmake command for the installation
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
> -DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> -DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs
>
> I have not seen any errors during installation.
>
> Thanks.
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 7 Sep 2017 15:51:39 -0400
> From: Wes Barnett <w.barnett at columbia.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gromacs installation
> Message-ID:
>         <CALkN6e1jd2y0iDMdjaq92Nu8uhUD3hTze5rscB1_S3kKCaeRsw at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Thu, Sep 7, 2017 at 3:25 PM, vijayakumar gosu <
> vijayakumargosu at gmail.com>
> wrote:
>
> > Hi,
> >
> > I have installed gromacs 5.1 in server which has 4 nodes each with 40
> cpus.
> > I am allotted to use only 2 nodes with 80 cpus. after installation when i
> > did sample md run only 20 cpus are being utilized. How can I fully
> utilize
> > the all 80 CPUs for mdrun.
> >
> > I have used below cmake command for the installation
> >
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
> > -DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> > -DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs
> >
> > I have not seen any errors during installation.
> >
>
> You should go ahead and just install 2016.3 instead of 5.1.
>
> What is your exact command when you run mdrun?
>
> --
> James "Wes" Barnett
> Postdoctoral Research Scientist
> Department of Chemical Engineering
> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
> Columbia University
> w.barnett at columbia.edu
> http://wbarnett.us
>
>
> ------------------------------
>
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> * Please search the archive at http://www.gromacs.org/
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> End of gromacs.org_gmx-users Digest, Vol 161, Issue 20
> ******************************************************
>