[gmx-users] gromacs.org_gmx-users Digest, Vol 166, Issue 49
sanjeet kumar singh ch16d012
ch16d012 at smail.iitm.ac.in
Sat Feb 10 11:32:15 CET 2018
Hello Krzysztof Makuch,
Thanks a lot for your valuable suggestion.
Cheers,
SK
On Sat, Feb 10, 2018 at 5:00 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Gromacs 2018 installation failed (Elton Carvalho)
> 2. Re: Gromacs 2018 installation failed (Elton Carvalho)
> 3. Re: Gromacs 2018 installation failed (Qinghua Liao)
> 4. Re: Do i need to put POSITION RESTRAINT DURING EQUILIBRATION
> STAGE ( NVT&NPT ) if i am preparing an amorphous sample?
> (Krzysztof Makuch)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 9 Feb 2018 20:33:41 -0200
> From: Elton Carvalho <eltonfc at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Gromacs 2018 installation failed
> Message-ID:
> <CAOYvBoLs8o5WQWNCcohV_UeLJhrCcb14pgS_e6oKDM-saySrnQ@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> If you are in a hurry, you can download the binutils package from here
> https://www.gnu.org/software/binutils/ and compile it on your own, setting
> the PREFIX to a directory in your home, then use $PATH to make your binary
> the highest priority.
>
> Cheers,
> Elton
>
> On Fri, Feb 9, 2018 at 8:17 PM, Qinghua Liao <scorpio.liao at gmail.com>
> wrote:
>
> > Hello Elton,
> >
> > Thanks a lot for your information, I already sent an e-mail to the
> > administrator,
> > hopefully they will fix it.
> >
> >
> > All the best,
> > Qinghua
> >
> >
> > On 02/09/2018 08:03 PM, Elton Carvalho wrote:
> >
> >> Hello, Qinghua,
> >>
> >> The error message refers to the standard library. I believe the package
> >> that provides this in ubuntu is glibc. Check that it's a current enough
> >> version.
> >>
> >> Another thing is that the liker (ld) needs to support C++11. That's the
> >> binutils package. I've had success with version 2.29. Not sure which is
> >> the
> >> lowest version required.
> >>
> >> Good luck,
> >> Elton
> >>
> >> On Fri, Feb 9, 2018 at 12:25 PM, Qinghua Liao <scorpio.liao at gmail.com>
> >> wrote:
> >>
> >> Dear GMX developers,
> >>>
> >>> I am trying to install Gromacs2018 with cuda on clusters, the
> >>> installation
> >>> was successful on one cluster,
> >>> but failed on the other cluster. I guess there might be some library
> >>> missing on the other cluster.
> >>>
> >>> For the succeeded one, the operating system is openSUSE 42.2 (GNU/Linux
> >>> 4.4.27-2-default), the compilers are gcc and c++ 4.8.5,
> >>> the CUDA version is 9.0.176, the MPI is openMPI 1.10.3
> >>>
> >>> For the failed one, the operating system is Ubuntu 16.04.3 (GNU/Linux
> >>> 4.4.0-109-generic x86_64), I tried CUDA 9.1.85 and 9.0.176,
> >>> together with gcc/c++ version 6.4, icc/icpc 2017.4, all were failed.
> The
> >>> error is the same:
> >>>
> >>>
> >>> -- Performing Test CXX11_STDLIB_PRESENT
> >>> -- Performing Test CXX11_STDLIB_PRESENT - Failed
> >>> CMake Error at cmake/gmxTestCXX11.cmake:210 (message):
> >>> This version of GROMACS requires C++11-compatible standard library.
> >>> Please
> >>> use a newer compiler, and/or a newer standard library, or use the
> >>> GROMACS
> >>> 5.1.x release. Consult the installation guide for details before
> >>> upgrading
> >>> components.
> >>> Call Stack (most recent call first):
> >>> CMakeLists.txt:168 (gmx_test_cxx11)
> >>>
> >>>
> >>> Here is my command:
> >>> CC=gcc CXX=c++ .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON
> >>> -DCMAKE_INSTALL_PREFIX=/--PATH--/Programs/Gromacs2018
> >>>
> >>> I am confused here that the old compilers worked but the new ones did
> >>> not,
> >>> while the error message suggests to use newer compilers.
> >>> Could some one help me with fixing it? Thanks a lot!
> >>>
> >>>
> >>> All the best,
> >>> Qinghua
> >>> --
> >>> 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
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >>
> >>
> >>
> >>
> > --
> > 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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Elton Carvalho
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 9 Feb 2018 20:33:41 -0200
> From: Elton Carvalho <eltonfc at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Gromacs 2018 installation failed
> Message-ID:
> <CAOYvBoLs8o5WQWNCcohV_UeLJhrCcb14pgS_e6oKDM-saySrnQ@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> If you are in a hurry, you can download the binutils package from here
> https://www.gnu.org/software/binutils/ and compile it on your own, setting
> the PREFIX to a directory in your home, then use $PATH to make your binary
> the highest priority.
>
> Cheers,
> Elton
>
> On Fri, Feb 9, 2018 at 8:17 PM, Qinghua Liao <scorpio.liao at gmail.com>
> wrote:
>
> > Hello Elton,
> >
> > Thanks a lot for your information, I already sent an e-mail to the
> > administrator,
> > hopefully they will fix it.
> >
> >
> > All the best,
> > Qinghua
> >
> >
> > On 02/09/2018 08:03 PM, Elton Carvalho wrote:
> >
> >> Hello, Qinghua,
> >>
> >> The error message refers to the standard library. I believe the package
> >> that provides this in ubuntu is glibc. Check that it's a current enough
> >> version.
> >>
> >> Another thing is that the liker (ld) needs to support C++11. That's the
> >> binutils package. I've had success with version 2.29. Not sure which is
> >> the
> >> lowest version required.
> >>
> >> Good luck,
> >> Elton
> >>
> >> On Fri, Feb 9, 2018 at 12:25 PM, Qinghua Liao <scorpio.liao at gmail.com>
> >> wrote:
> >>
> >> Dear GMX developers,
> >>>
> >>> I am trying to install Gromacs2018 with cuda on clusters, the
> >>> installation
> >>> was successful on one cluster,
> >>> but failed on the other cluster. I guess there might be some library
> >>> missing on the other cluster.
> >>>
> >>> For the succeeded one, the operating system is openSUSE 42.2 (GNU/Linux
> >>> 4.4.27-2-default), the compilers are gcc and c++ 4.8.5,
> >>> the CUDA version is 9.0.176, the MPI is openMPI 1.10.3
> >>>
> >>> For the failed one, the operating system is Ubuntu 16.04.3 (GNU/Linux
> >>> 4.4.0-109-generic x86_64), I tried CUDA 9.1.85 and 9.0.176,
> >>> together with gcc/c++ version 6.4, icc/icpc 2017.4, all were failed.
> The
> >>> error is the same:
> >>>
> >>>
> >>> -- Performing Test CXX11_STDLIB_PRESENT
> >>> -- Performing Test CXX11_STDLIB_PRESENT - Failed
> >>> CMake Error at cmake/gmxTestCXX11.cmake:210 (message):
> >>> This version of GROMACS requires C++11-compatible standard library.
> >>> Please
> >>> use a newer compiler, and/or a newer standard library, or use the
> >>> GROMACS
> >>> 5.1.x release. Consult the installation guide for details before
> >>> upgrading
> >>> components.
> >>> Call Stack (most recent call first):
> >>> CMakeLists.txt:168 (gmx_test_cxx11)
> >>>
> >>>
> >>> Here is my command:
> >>> CC=gcc CXX=c++ .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON
> >>> -DCMAKE_INSTALL_PREFIX=/--PATH--/Programs/Gromacs2018
> >>>
> >>> I am confused here that the old compilers worked but the new ones did
> >>> not,
> >>> while the error message suggests to use newer compilers.
> >>> Could some one help me with fixing it? Thanks a lot!
> >>>
> >>>
> >>> All the best,
> >>> Qinghua
> >>> --
> >>> 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
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >>
> >>
> >>
> >>
> > --
> > 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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Elton Carvalho
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 9 Feb 2018 23:36:57 +0100
> From: Qinghua Liao <scorpio.liao at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Gromacs 2018 installation failed
> Message-ID: <c04c3bde-1f96-6021-04bd-1d09764624f0 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello Elton,
>
> Thanks a lot for your help! I just tried to load a binutils library (it
> was installed on the cluster) and install Gromacs 2018 again,
> it works now!
>
>
> All the best,
> Qinghua
>
>
> On 02/09/2018 11:33 PM, Elton Carvalho wrote:
> > If you are in a hurry, you can download the binutils package from here
> > https://www.gnu.org/software/binutils/ and compile it on your own,
> setting
> > the PREFIX to a directory in your home, then use $PATH to make your
> binary
> > the highest priority.
> >
> > Cheers,
> > Elton
> >
> > On Fri, Feb 9, 2018 at 8:17 PM, Qinghua Liao <scorpio.liao at gmail.com>
> wrote:
> >
> >> Hello Elton,
> >>
> >> Thanks a lot for your information, I already sent an e-mail to the
> >> administrator,
> >> hopefully they will fix it.
> >>
> >>
> >> All the best,
> >> Qinghua
> >>
> >>
> >> On 02/09/2018 08:03 PM, Elton Carvalho wrote:
> >>
> >>> Hello, Qinghua,
> >>>
> >>> The error message refers to the standard library. I believe the package
> >>> that provides this in ubuntu is glibc. Check that it's a current enough
> >>> version.
> >>>
> >>> Another thing is that the liker (ld) needs to support C++11. That's the
> >>> binutils package. I've had success with version 2.29. Not sure which is
> >>> the
> >>> lowest version required.
> >>>
> >>> Good luck,
> >>> Elton
> >>>
> >>> On Fri, Feb 9, 2018 at 12:25 PM, Qinghua Liao <scorpio.liao at gmail.com>
> >>> wrote:
> >>>
> >>> Dear GMX developers,
> >>>> I am trying to install Gromacs2018 with cuda on clusters, the
> >>>> installation
> >>>> was successful on one cluster,
> >>>> but failed on the other cluster. I guess there might be some library
> >>>> missing on the other cluster.
> >>>>
> >>>> For the succeeded one, the operating system is openSUSE 42.2
> (GNU/Linux
> >>>> 4.4.27-2-default), the compilers are gcc and c++ 4.8.5,
> >>>> the CUDA version is 9.0.176, the MPI is openMPI 1.10.3
> >>>>
> >>>> For the failed one, the operating system is Ubuntu 16.04.3 (GNU/Linux
> >>>> 4.4.0-109-generic x86_64), I tried CUDA 9.1.85 and 9.0.176,
> >>>> together with gcc/c++ version 6.4, icc/icpc 2017.4, all were failed.
> The
> >>>> error is the same:
> >>>>
> >>>>
> >>>> -- Performing Test CXX11_STDLIB_PRESENT
> >>>> -- Performing Test CXX11_STDLIB_PRESENT - Failed
> >>>> CMake Error at cmake/gmxTestCXX11.cmake:210 (message):
> >>>> This version of GROMACS requires C++11-compatible standard
> library.
> >>>> Please
> >>>> use a newer compiler, and/or a newer standard library, or use the
> >>>> GROMACS
> >>>> 5.1.x release. Consult the installation guide for details before
> >>>> upgrading
> >>>> components.
> >>>> Call Stack (most recent call first):
> >>>> CMakeLists.txt:168 (gmx_test_cxx11)
> >>>>
> >>>>
> >>>> Here is my command:
> >>>> CC=gcc CXX=c++ .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON
> >>>> -DCMAKE_INSTALL_PREFIX=/--PATH--/Programs/Gromacs2018
> >>>>
> >>>> I am confused here that the old compilers worked but the new ones did
> >>>> not,
> >>>> while the error message suggests to use newer compilers.
> >>>> Could some one help me with fixing it? Thanks a lot!
> >>>>
> >>>>
> >>>> All the best,
> >>>> Qinghua
> >>>> --
> >>>> 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
> >>>>
> >>>> * For (un)subscribe requests visit
> >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>>> send a mail to gmx-users-request at gromacs.org.
> >>>>
> >>>
> >>>
> >>>
> >> --
> >> 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
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 10 Feb 2018 00:30:28 +0100
> From: Krzysztof Makuch <krzysztof.makuch at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Do i need to put POSITION RESTRAINT DURING
> EQUILIBRATION STAGE ( NVT&NPT ) if i am preparing an amorphous
> sample?
> Message-ID:
> <CAA-L7o56XAORg6EhfbyMGrj0LkFGgKtfysBZnFObRD+YHA=b+g at mail.gmail.
> com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
> That's always your call. You perform equilibration to swap between MM
> (energy minimization) and MD (kinetic energy). In the other word you slowly
> start MD and prevent unwanted and unrealistic rearrangement in your system.
> If initial positions are important - you restrain the interesting
> molecules. If you equilibrate for example lipid bilayer - there is no
> reason to do that. Often you can also totally skip equilibration and just
> cut off a few initial ns. Sometimes you make nvt, npt and still cut off
> beginning and sometimes you perform MD to find optimal system, in which
> case the whole simulation is in fact equilibration.
> You know your system, you have to consider if restraining movement is what
> you need.
> Best,
> KM
>
> 2018-02-09 13:28 GMT+01:00 sanjeet kumar singh ch16d012 <
> ch16d012 at smail.iitm.ac.in>:
>
> > Hi list,
> >
> > I am preparing an amorphous sample using GROMACS but i am in doubt that
> > during the equilibration stage ( NVT & NPT ) do i need to put position
> > restraint on my polymer as there are no solvent in my system and if i
> have
> > to use position restraint then why i should do that?
> >
> > THANKS,
> > SK
> > --
> > 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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Jagiellonian University
> Department of Computational Biophysics and Bioinformatics
> tel.1: (12) 664 61 49
> tel.2: (48) 664 086 049
>
>
> ------------------------------
>
> --
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 166, Issue 49
> ******************************************************
>
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