Re: [gmx-users] interfacing with Gaussian 09 (Mark Abraham) (Groenhof, Gerrit)

[Andrian Saputra]

Make it easy with ORCA
Pada tanggal 14 Jun 2016 05.19, "Clinton King" 
menulis:

> Gerrit,
>
> Thanks for your suggestions. I am using GROMACS 5.1.2.
>
> After reading through your message, I realized that I was using GAUSS_DIR
> and GAUSS_EXE for the location and name of the gau script instead of
> GMX_QM_GAUSS_DIR and GMX_QM_GAUSS_EXE. So I changed that, and then I got
> the error message from line 227 of qm_gaussian.c : "no
> $GMX_QM_MODIFIED_LINKS_DIR, this is were the modified links reside."
>
> I thought that one could use the gau script successfully without modifying
> any Gaussian links.
>
> I decided to try setting the GMX_QM_MODIFIED_LINKS_DIR environmental
> variable to an empty folder. I am attaching the resulting output (as links
> at the end of this message); both what was sent to stdout as well as the
> gmx generated log file.
>
> Looking through qm_gaussian.c, as well as the output I have so far, it
> appears that modified Gaussian links *are* required for gmx to interface
> with Gaussian.
>
> So, the bottom line is that in order for Gromacs to interface with Gaussian
> to perform a quantum molecular dynamics computation, I must have access to
> the Gaussian source code. Is that correct?
>
>
> https://drive.google.com/file/d/0B-W4G39j_Icjc21TcTN1S2M0MVk/view?usp=sharing
>
> https://drive.google.com/file/d/0B-W4G39j_IcjZlVPb1NySkUtRDQ/view?usp=sharing
>
> (Please let me know if the links above don't work.)
>
> Thanks for your help
>
> --
> Clinton King
> Graduate Student
> Chemistry Department
> Brigham Young University
>
>
> > Message: 2
> > Date: Sun, 12 Jun 2016 05:16:13 +
> > From: "Groenhof, Gerrit" 
> > To: "gromacs.org_gmx-users@maillist.sys.kth.se"
> > 
> > Subject: Re: [gmx-users] interfacing with Gaussian 09 (Mark Abraham)
> > Message-ID:
> > <
> 858a7947bc0fe04da05e1786a6d51d45263d6...@um-excdag-a05.um.gwdg.de
> > >
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Hi,
> >
> > Which version of Gmx are you using?
> >
> > I ask because of a recent bug fix. The bug was that I tried to print the
> > value of an environment variable, without checking if that variable was
> > set, causing set faulting.
> >
> > Make sure the GMX_QM_GAUSS_DIR (for Gmx < 5 GAUSS_DIR) are set and point
> > to the location of the g09 directory.
> >
> > IN any case, for normal gaussian runs, the program should not write out
> > the LJ.dat. IF the above does not help, you could perhaps send me the
> input
> > (off list) and I can have a look at what goes wrong.
> >
> > Best,
> >
> > Gerrit
> >
> >
> >
> > Hi,
> >
> > Please don't subscribe to a digest if you're planning to reply to the
> > digest and de-thread the discussion. Gerrit said the other week that gau
> > works.
> >
> > Mark
> >
> > On Fri, 10 Jun 2016 18:18 Mark Abraham  wrote:
> >
> > > Hi,
> > >
> > > Please check out http://wwwuser.gwdg.de/~ggroenh/qmmm.html and
> > >
> >
> http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM
> > >
> > > Mark
> > >
> > > On Fri, Jun 10, 2016 at 5:13 PM Clinton King <
> clintonkin...@chem.byu.edu
> > >
> > > wrote:
> > >
> > >> I'm having difficulty interfacing GROMACS with Gaussian 09. Is there
> > >> anyone
> > >> who has successfully done it who is willing to give some advice?
> > >>
> > >> --
> > >> Clinton King
> > >> Graduate Student
> > >> Chemistry Department
> > >> Brigham Young University
> > >> --
> > >> 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-requ...@gromacs.org.
> > >>
> > >
> >
> >
> > --
> >
> > Message: 2
> > Date: Fri, 10 Jun 2016 14:27:01 -0600
> > From: Clinton King 
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: Re: [gmx-users] interfacing with Gaussian 09
> > Message-ID:
> > 

Re: [gmx-users] installation of gromacs as parallel in a system without access to root

[Andrian Saputra]

You have not installed fftw yet...
Pada tanggal 13 Jun 2016 13.53, "Atila Petrosian" 
menulis:

> Dear Mark,
>
> Thanks for your quick answer.
>
> In this case, after using your suggested command:
>
> cmake .. -DGMX_GPU=ON -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/home/marydoe/programs
>
> Should I use following commands?
>
> make check
> make install
> source /home/marydoe/programs/gromacs/bin/GMXRC
>
> Are these commands enough for complete installation?
>
> Best,
> Atila
> --
> 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-requ...@gromacs.org.
>
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Re: [gmx-users] problem compiling template

[Andrian Saputra]

Use
-dfftw_library=/path/to/libfftw3.so
-dfftw_include_dir=path/to/includedirectory
Pada tanggal 12 Jun 2016 21.55, "Teemu Murtola" 
menulis:

> Hi,
>
> On Fri, Jun 10, 2016 at 8:51 PM Michael Brunsteiner <
> michael.brunstei...@tugraz.at> wrote:
>
> > I just installed a pristine gromacs 5.1.2, on my lubuntu 64bit vanilla
> > desktop, as in:
> >
> > prompt> cmake .. -DGMX_GPU=ON
> > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.2-bin
> -DGMX_BUILD_OWN_FFTW=ON
> > prompt> make -j 6
> > prompt> make install
> >
> > this worked ... then if I go to the resulting
> > /usr/local/gromacs-5.1.2-bin/share/gromacs/template
> > and say (as recommended in the README file there)
> >
> > prompt> . /usr/local/gromacs-5.1.2-bin/bin/GMXRC.bash
> > prompt> cmake .
> >
> > I get:
> >
> > prompt> make
> > Linking CXX executable template
> > /usr/bin/ld: cannot find -lgmxfftw
> > collect2: error: ld returned 1 exit status
> > make[2]: *** [template] Error 1
> > make[1]: *** [CMakeFiles/template.dir/all] Error 2
> > make: *** [all] Error 2
> >
>
> Yes, this is a documented limitation at <
>
> http://manual.gromacs.org/documentation/5.1.2/doxygen/html-user/page_usinglibrary.xhtml
> >.
> You can either use the Makefile.pkg installed with the template (if you
> have pkg-config), or you can build Gromacs with GMX_BUILD_OWN_FFTW=OFF.
>
> if I do the same not in the installation but in the distribution
> > directory then I get:
> >
> > prompt> make
> > [100%] Building CXX object CMakeFiles/template.dir/template.o
> > /usr/local/software/gromacs-5.1.2/share/template/template.cpp:38:40:
> > fatal error: gromacs/trajectoryanalysis.h: No such file or directory
> >   #include 
> >  ^
> > compilation terminated.
> >
>
> Most likely, you should install a separate gromacs-dev package or similar
> from your distribution, since the headers might be packaged in such.
> Ideally, the template should also get installed from the development
> package, since it is not really useful without.
>
> Best regards,
> Teemu
> --
> 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-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] installation error gromacs-imd

[Andrian Saputra]

Thanks Mark...
Pada tanggal 9 Jun 2016 18.58, "Mark Abraham" <mark.j.abra...@gmail.com>
menulis:

> Hi,
>
> Please use a released version of GROMACS and don't smash your OS by running
> make with sudo. Then we can consider problems that may arise :-)
>
> Mark
>
> On Thu, 9 Jun 2016 11:30 Andrian Saputra <andrian.c...@gmail.com> wrote:
>
> > Hi..May be its not a gromacs master..
> > But i think there is no problem with source
> > Pada tanggal 9 Jun 2016 15.48, "Kutzner, Carsten" <ckut...@gwdg.de>
> > menulis:
> >
> > >
> > > > On 09 Jun 2016, at 09:33, Andrian Saputra <andrian.c...@gmail.com>
> > > wrote:
> > > >
> > > > Hi,,
> > > >
> > > > Ya i hve tried to install version 5.0 and all compilation is ok...
> but
> > i
> > > > familiar with version 4.5, 4.6... version 5.0 need some changes in
> mdp
> > > > file...
> > > But isn't this the master version of GROMACS that you tried to compile?
> > > For that version you will probably have to do some more adaptations of
> > > your .mdp file.
> > >
> > > There is no IMD for 4.5 and 4.6, you will need to use 5.0 or later.
> > >
> > > Carsten
> > >
> > > >
> > > > Do you have idea about the error ??
> > > >
> > > > Thank you
> > > > Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten" <ckut...@gwdg.de>
> > > menulis:
> > > >
> > > >> Hi,
> > > >>
> > > >> the error message you see has nothing to do with IMD. Have you tried
> > > >> to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
> > > >> work out of the box with IMD.
> > > >>
> > > >> Best,
> > > >>  Carsten
> > > >>
> > > >>
> > > >>> On 09 Jun 2016, at 04:35, Andrian Saputra <andrian.c...@gmail.com>
> > > >> wrote:
> > > >>>
> > > >>> Dear gromacs users
> > > >>>
> > > >>> i was trying to install gromacs-imd that was developed by Martin
> > > Hoefling
> > > >>> http://www.mpibpc.mpg.de/grubmueller/interactivemd
> > > >>>
> > > >>> all configuration is ok with this command:
> > > >>>
> > > >>> CC=$HOME/software/openmpi/bin/mpicc
> > > >>> CXX=$HOME/software/openmpi/bin/mpicxx
> > > >>> F77=$HOME/software/openmpi/bin/mpif77
> > > >>> F90=$HOME/software/openmpi/bin/mpif90
> > > >>>
> > CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
> > > >>>
> > > >>
> > >
> >
> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
> > > >>>
> > > >>>
> > > >>
> > >
> >
> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
> > > >>>
> > > >>> cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
> > > >>> -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs
> -DGMX_INTERNAL_BOOST=ON
> > > >>> -DGMX_QMMM_PROGRAM=ORCA
> > > >>> -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a
> -Wno-dev
> > > >>>
> > > >>> after i execute sudo make -j4, i got this error message:
> > > >>>
> > > >>>
> > > >>
> > >
> >
> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
> > > >>> error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
> > > >>>*z3 = gmx_mm256_set_m128(tz,tz);
> > > >>> .
> > > >>> .
> > > >>> .
> > > >>> .bla bla bla...
> > > >>> src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for
> > > target
> > > >>>
> > > >>
> > >
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
> > > >>> failed
> > > >>> make[2]: ***
> > > >>>
> > > >>
> > >
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW

Re: [gmx-users] installation error gromacs-imd

[Andrian Saputra]

Hi..May be its not a gromacs master..
But i think there is no problem with source
Pada tanggal 9 Jun 2016 15.48, "Kutzner, Carsten" <ckut...@gwdg.de> menulis:

>
> > On 09 Jun 2016, at 09:33, Andrian Saputra <andrian.c...@gmail.com>
> wrote:
> >
> > Hi,,
> >
> > Ya i hve tried to install version 5.0 and all compilation is ok... but i
> > familiar with version 4.5, 4.6... version 5.0 need some changes in mdp
> > file...
> But isn't this the master version of GROMACS that you tried to compile?
> For that version you will probably have to do some more adaptations of
> your .mdp file.
>
> There is no IMD for 4.5 and 4.6, you will need to use 5.0 or later.
>
> Carsten
>
> >
> > Do you have idea about the error ??
> >
> > Thank you
> > Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten" <ckut...@gwdg.de>
> menulis:
> >
> >> Hi,
> >>
> >> the error message you see has nothing to do with IMD. Have you tried
> >> to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
> >> work out of the box with IMD.
> >>
> >> Best,
> >>  Carsten
> >>
> >>
> >>> On 09 Jun 2016, at 04:35, Andrian Saputra <andrian.c...@gmail.com>
> >> wrote:
> >>>
> >>> Dear gromacs users
> >>>
> >>> i was trying to install gromacs-imd that was developed by Martin
> Hoefling
> >>> http://www.mpibpc.mpg.de/grubmueller/interactivemd
> >>>
> >>> all configuration is ok with this command:
> >>>
> >>> CC=$HOME/software/openmpi/bin/mpicc
> >>> CXX=$HOME/software/openmpi/bin/mpicxx
> >>> F77=$HOME/software/openmpi/bin/mpif77
> >>> F90=$HOME/software/openmpi/bin/mpif90
> >>> CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
> >>>
> >>
> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
> >>>
> >>>
> >>
> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
> >>>
> >>> cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
> >>> -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs -DGMX_INTERNAL_BOOST=ON
> >>> -DGMX_QMMM_PROGRAM=ORCA
> >>> -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a -Wno-dev
> >>>
> >>> after i execute sudo make -j4, i got this error message:
> >>>
> >>>
> >>
> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
> >>> error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
> >>>*z3 = gmx_mm256_set_m128(tz,tz);
> >>> .
> >>> .
> >>> .
> >>> .bla bla bla...
> >>> src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for
> target
> >>>
> >>
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
> >>> failed
> >>> make[2]: ***
> >>>
> >>
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
> >>> Error 1
> >>> CMakeFiles/Makefile2:1586: recipe for target
> >>> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> >>> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> >>> Makefile:160: recipe for target 'all' failed
> >>> make: *** [all] Error 2
> >>>
> >>>
> >>> anyone can suggest me to solve this errro ? thank you so much
> >>> --
> >>> --
> >>> 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-requ...@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
> &g

Re: [gmx-users] installation error gromacs-imd

[Andrian Saputra]

Hi,,

Ya i hve tried to install version 5.0 and all compilation is ok... but i
familiar with version 4.5, 4.6... version 5.0 need some changes in mdp
file...

Do you have idea about the error ??

Thank you
Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten" <ckut...@gwdg.de> menulis:

> Hi,
>
> the error message you see has nothing to do with IMD. Have you tried
> to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
> work out of the box with IMD.
>
> Best,
>   Carsten
>
>
> > On 09 Jun 2016, at 04:35, Andrian Saputra <andrian.c...@gmail.com>
> wrote:
> >
> > Dear gromacs users
> >
> > i was trying to install gromacs-imd that was developed by Martin Hoefling
> > http://www.mpibpc.mpg.de/grubmueller/interactivemd
> >
> > all configuration is ok with this command:
> >
> > CC=$HOME/software/openmpi/bin/mpicc
> > CXX=$HOME/software/openmpi/bin/mpicxx
> > F77=$HOME/software/openmpi/bin/mpif77
> > F90=$HOME/software/openmpi/bin/mpif90
> > CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
> >
> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
> >
> >
> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
> >
> > cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
> > -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs -DGMX_INTERNAL_BOOST=ON
> > -DGMX_QMMM_PROGRAM=ORCA
> > -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a -Wno-dev
> >
> > after i execute sudo make -j4, i got this error message:
> >
> >
> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
> > error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
> > *z3 = gmx_mm256_set_m128(tz,tz);
> > .
> > .
> > .
> > .bla bla bla...
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for target
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
> > failed
> > make[2]: ***
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
> > Error 1
> > CMakeFiles/Makefile2:1586: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:160: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> >
> > anyone can suggest me to solve this errro ? thank you so much
> > --
> > --
> > 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-requ...@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-requ...@gromacs.org.
-- 
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[gmx-users] installation error gromacs-imd

[Andrian Saputra]

Dear gromacs users

i was trying to install gromacs-imd that was developed by Martin Hoefling
http://www.mpibpc.mpg.de/grubmueller/interactivemd

all configuration is ok with this command:

CC=$HOME/software/openmpi/bin/mpicc
CXX=$HOME/software/openmpi/bin/mpicxx
F77=$HOME/software/openmpi/bin/mpif77
F90=$HOME/software/openmpi/bin/mpif90
CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib

CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include

cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
-DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs -DGMX_INTERNAL_BOOST=ON
-DGMX_QMMM_PROGRAM=ORCA
-DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a -Wno-dev

after i execute sudo make -j4, i got this error message:

/home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
 *z3 = gmx_mm256_set_m128(tz,tz);
.
.
.
.bla bla bla...
src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
failed
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
Error 1
CMakeFiles/Makefile2:1586: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2


anyone can suggest me to solve this errro ? thank you so much
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Re: [gmx-users] top parameters for pluronic f127 (Andrian Saputra)

[Andrian Saputra]

Hi.. i think it is not a problem.. according to the previous question, i
think we can use and calculate charges for non-optimized structure (as a
initial charge) and then re-update charges for each optimization process...
in this case, using website atomicchargecalculator will not be a problem..

Cheers
Pada tanggal 5 Jun 2016 20.28, "ABEL Stephane 175950" <stephane.a...@cea.fr>
menulis:

> Hi,
>
> Before to compute the partial charges , you have to optimize the molecule.
> It may be very difficult if you have a large molecule (> 100 atoms). So for
> polymers with reapeated units, it is always advisable to separate the
> molecule into similar molecular blocks. It is straighforward for pluronic
> f127.  To derive charges for AMBER simulations, you can use the RED server*
> and checkout the detailed tutorials. It is an advanced topic
>
> http://upjv.q4md-forcefieldtools.org/REDServer-Development/
>
> Good luck,
>
>
> 
> Stéphane Abel, Ph.D.
>
> CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 9198
> Institut de Biologie Intégrative de la Cellule (I2BC)
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
>
> 
> De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] de la part de
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se [
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se]
> Envoyé : dimanche 5 juin 2016 12:00
> À : gromacs.org_gmx-users@maillist.sys.kth.se
> Objet : gromacs.org_gmx-users Digest, Vol 146, Issue 24
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> Today's Topics:
>
>1. Re: top parameters for pluronic f127 (Andrian Saputra)
>2. Re: top parameters for pluronic f127 (Andrian Saputra)
>
>
> --
>
> Message: 1
> Date: Sun, 5 Jun 2016 10:52:52 +0700
> From: Andrian Saputra <andrian.c...@gmail.com>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] top parameters for pluronic f127
> Message-ID:
> <
> calw802k-qyfemakgx52yf5wspxm66s5q9ghtud3m6gmh6r-...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I have the same problem.. but gasteiger is less accurate... anyone can
> suggest software quickly generating am1bcc, resp, esp charges for big
> molecules ?
> Pada tanggal 4 Jun 2016 00.51, "Alan" <alanwil...@gmail.com> menulis:
>
> > It's too big! It will never work.
> >
> > Try the following alternatives:
> > - to use gasteiger charge (and then you get only the topology);
> > - as you said it's a polymer, take the smallest common unit, join 3
> pieces
> > of it and get the topology/charges for it, use the middle unit to extend
> > the charge for all internal units of your polymer and the extreme to
> model
> > your terminals.
> >
> > Good luck,
> >
> > Alan
> >
> > On 3 June 2016 at 18:37, SAKO MIRZAIE <sako.bioc...@gmail.com> wrote:
> >
> > > Dear All,
> > >
> > > I am trying to convert my mol2 file to amber99sb itp to do MD by
> > > gromacs. but, when I use ACPYPE software, it run and never finished.
> > > my mol2 file is pluronic F127 and contains 2500 atoms. this structure
> > > is a polymer and huge in size. how can I get an itp file for my
> > > polymer? How can I simulate it in MD by gromacs? do polymers have some
> > > tricks?
> > >
> > > the molecular structure of f127 is: A99B67A99
> > >
> > > where
> > >
> > > A: ethylene oxide
> > > B: propylene oxide
> > >
> > > best regards,
> > >
> > > --
> > > ***
> > > sako mirzaie
> > > PhD in biochemistry
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/

Re: [gmx-users] top parameters for pluronic f127

[Andrian Saputra]

I got the idea...
May be you can consider this webpage:

webchem.ncbr.muni.cz/Platform/ChargeCalculator#bio-more

For efficiently generating charges into large molecules
Pada tanggal 5 Jun 2016 10.52, "Andrian Saputra" <andrian.c...@gmail.com>
menulis:

> I have the same problem.. but gasteiger is less accurate... anyone can
> suggest software quickly generating am1bcc, resp, esp charges for big
> molecules ?
> Pada tanggal 4 Jun 2016 00.51, "Alan" <alanwil...@gmail.com> menulis:
>
>> It's too big! It will never work.
>>
>> Try the following alternatives:
>> - to use gasteiger charge (and then you get only the topology);
>> - as you said it's a polymer, take the smallest common unit, join 3 pieces
>> of it and get the topology/charges for it, use the middle unit to extend
>> the charge for all internal units of your polymer and the extreme to model
>> your terminals.
>>
>> Good luck,
>>
>> Alan
>>
>> On 3 June 2016 at 18:37, SAKO MIRZAIE <sako.bioc...@gmail.com> wrote:
>>
>> > Dear All,
>> >
>> > I am trying to convert my mol2 file to amber99sb itp to do MD by
>> > gromacs. but, when I use ACPYPE software, it run and never finished.
>> > my mol2 file is pluronic F127 and contains 2500 atoms. this structure
>> > is a polymer and huge in size. how can I get an itp file for my
>> > polymer? How can I simulate it in MD by gromacs? do polymers have some
>> > tricks?
>> >
>> > the molecular structure of f127 is: A99B67A99
>> >
>> > where
>> >
>> > A: ethylene oxide
>> > B: propylene oxide
>> >
>> > best regards,
>> >
>> > --
>> > ***
>> > sako mirzaie
>> > PhD in biochemistry
>> > --
>> > 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-requ...@gromacs.org.
>> >
>>
>>
>>
>> --
>> Alan Wilter SOUSA da SILVA, DSc
>> Senior Bioinformatician, UniProt
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> United Kingdom
>> Tel: +44 (0)1223 494588
>> --
>> 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-requ...@gromacs.org.
>>
>
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Re: [gmx-users] top parameters for pluronic f127

[Andrian Saputra]

I have the same problem.. but gasteiger is less accurate... anyone can
suggest software quickly generating am1bcc, resp, esp charges for big
molecules ?
Pada tanggal 4 Jun 2016 00.51, "Alan"  menulis:

> It's too big! It will never work.
>
> Try the following alternatives:
> - to use gasteiger charge (and then you get only the topology);
> - as you said it's a polymer, take the smallest common unit, join 3 pieces
> of it and get the topology/charges for it, use the middle unit to extend
> the charge for all internal units of your polymer and the extreme to model
> your terminals.
>
> Good luck,
>
> Alan
>
> On 3 June 2016 at 18:37, SAKO MIRZAIE  wrote:
>
> > Dear All,
> >
> > I am trying to convert my mol2 file to amber99sb itp to do MD by
> > gromacs. but, when I use ACPYPE software, it run and never finished.
> > my mol2 file is pluronic F127 and contains 2500 atoms. this structure
> > is a polymer and huge in size. how can I get an itp file for my
> > polymer? How can I simulate it in MD by gromacs? do polymers have some
> > tricks?
> >
> > the molecular structure of f127 is: A99B67A99
> >
> > where
> >
> > A: ethylene oxide
> > B: propylene oxide
> >
> > best regards,
> >
> > --
> > ***
> > sako mirzaie
> > PhD in biochemistry
> > --
> > 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-requ...@gromacs.org.
> >
>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Software generating gaff for gromacs with am1bcc charges

[Andrian Saputra]

Thanks hannes, in my qmmm system, qm parts consist of 100 atoms...
Pada tanggal 3 Jun 2016 13.30, "Hannes Loeffler" <hannes.loeff...@stfc.ac.uk>
menulis:

> On Fri, 3 Jun 2016 12:47:34 +0700
> Andrian Saputra <andrian.c...@gmail.com> wrote:
>
> > Hi all, can anyone suggest me whats softwares can produce gaff
> > topology for gromacs with am1bcc charges automatically for 100-200
> > atoms ?
>
> All the software I'm aware of wraps around antechamber and so won't do
> any magic to fix problems with the input structure.  With that number
> of atoms I also wonder what that particular molecule is and whether
> you better split that into smaller pieces.
>
>
> > I tried antechamber and always found error...
>
> That's an entirely useless statement and nobody will be able to help
> you with that.  You may want to go through the relevant AMBER tutorial
> to learn how to use the tool and ask antechamber specific questions on
> the AMBER mailing list.
>
> --
> Gromacs Users mailing list
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[gmx-users] Software generating gaff for gromacs with am1bcc charges

[Andrian Saputra]

Hi all, can anyone suggest me whats softwares can produce gaff topology for
gromacs with am1bcc charges automatically for 100-200 atoms ?
I tried antechamber and always found error...

Thank you
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[gmx-users] warning 1-4 interaction in QMMM simulation

[andrian]

Dear gromacs users

i was trying to perform micro-iterative QMMM optimization using 
gromacs/orca interface... in mdp file, i set bOpt = yes, then i got a 
warning like this:


"Warning: 1-4 interaction between 3 and 6 at distance 3.565 which is 
larger than the 1-4 table size 2.000 nm, These are ignored for the rest 
of the simulation, This usually means your system is exploding, if not, 
you should increase table-extension in your mdp file, or with user 
tables increase the table size"


note: my sistem has been successfully minimized and also NVT restrained 
simulation...



anyone can help ? thank you so much..

cheers

***
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = steep

tinit= 0
dt   = 0.01
nsteps   = 100

nstcomm  = 1
comm_grps= system

emtol= 100.0
emstep   = 0.001

nstxout  = 1
nstvout  = 1
nstfout  = 1
nstlog   = 1
nstenergy= 1
nstxtcout= 1
xtc-precision= 1000
xtc_grps = system
energy_grps  = QMatoms MMatoms

nstlist  = 1
ns_type  = grid
pbc  = xyz
rlist= 1.0
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
epsilon_r= 1.0
fourierspacing  = 0.12
ewald_rtol = 1e-5

vdwtype  = Cut-off
rvdw = 1.0
DispCorr = No

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult   = 1
bOPT = yes
bTS  = no

constraints  = none


! AM1 PModel

%scf
  SCFMode Direct
  MaxIter 1500
  UseCheapInts true
end

qmmm.inp file produced by gromacs

#input-file generated by gromacs
!QMMMOpt TightSCF
! AM1 PModel


%scf
  SCFMode Direct
  MaxIter 1500
  UseCheapInts true
end
%geom
   Constraints
{C 0 C}
{C 8 C}
 end
   end
*xyz  1 1
  6 109.5018196  61.3748932  61.6309643
  1  2.3429996   2.3269998   2.5830004
  1  2.275   2.484   2.568
  6  2.4526897   2.4437210   2.4452071
  1  2.5284982   2.3686990   2.4200514
  8  2.5167450   2.5439975   2.5247785
  1  2.4429335   2.4939966   2.3479901
  1  2.4590001   2.579   2.5840002
  1 12.1445608  12.8626895  13.1234348
  8  2.7731431   2.5095880   2.3919705
  1  2.8239998   2.581   2.4270001
  1  2.696   2.5050002   2.464
  1  2.707   2.5490001   2.3260000
*

--
Andrian Saputra
Department of Pharmaceutical Science
Sumatera Institute of Technology, Indonesia

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[gmx-users] qmmm question

[andrian]

Dear gromacs users

in Dr Gerrits' qmmm tutorial, why section of [angles], [dihedrals] 
proper, & [dihedrals] improper in topology file for QM parts not ignores 
MM parameters ...?

it is only [bonds] section that ignores MM parameters..

anyone can explain ? Thank you

Cheers

--
Andrian Saputra
Department of Pharmaceutical Science
Sumatera Institute of Technology, Indonesia

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Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi,

anyone can help me ??? :(

On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian <andrian.c...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
   alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma
epsilon   Amb
   c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01
; 1.91  0.1094
   h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02
; 1.39  0.0157
   oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01
; 1.72  0.2104
   cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00
; 1.95  0.2650
   hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02
; 1.49  0.0157
   ho   ho  10.0  0.0   A 0.0e+00 0.0e+00
; 0.00  0.
   LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ moleculetype ]
;namenrexcl
   alkohol  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
   1   c3 1   UNL C1 0.122400 12.01000 ; qtot 0.122
   2   c3 1   UNLC12 0.015700 12.01000 

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi Gerrit and all users,

do you have an idea about this problem ? now, i attached all my 
simulation files... hope someone can help.. thanks in advance



cheers


On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian <andrian.c...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
   alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma
epsilon   Amb
   c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01
; 1.91  0.1094
   h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02
; 1.39  0.0157
   oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01
; 1.72  0.2104
   cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00
; 1.95  0.2650
   hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02
; 1.49  0.0157
   ho   ho  10.0  0.0   A 0.0e+00 0.0e+00
; 0.00  0.
   LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ moleculetype ]
;namenrexcl
   alkohol  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
   1   c3

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi Gerrit and all users,

do you have an idea about this problem ? now, i attached all my 
simulation files... hope someone can help.. thanks in advance



cheers


On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian <andrian.c...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
   alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma
epsilon   Amb
   c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01
; 1.91  0.1094
   h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02
; 1.39  0.0157
   oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01
; 1.72  0.2104
   cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00
; 1.95  0.2650
   hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02
; 1.49  0.0157
   ho   ho  10.0  0.0   A 0.0e+00 0.0e+00
; 0.00  0.
   LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ moleculetype ]
;namenrexcl
   alkohol  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
   1   c3

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi,

thank you for your kindly reply...

system has been successfully minimized, restrained NVT/NPT equilibrated, 
and unrestrained Classical MM before... there is no problem..


*
here is my equilibrated structure (strarting configuration for qmmm)
Grunge ROck MAChoS
   20
1UNL  C1   2.600   2.380   2.439
1UNL C12   2.540   2.521   2.421
1UNL  H3   2.554   2.304   2.376
1UNL  O4   2.587   2.339   2.575
1UNL H15   2.708   2.376   2.422
1UNL C26   2.388   2.522   2.440
1UNL H27   2.554   2.559   2.319
1UNL CL8   2.612   2.651   2.519
1UNL C39   2.327   2.649   2.379
1UNL H3   10   2.363   2.497   2.543
1UNL H4   11   2.354   2.441   2.375
1UNL H5   12   2.287   2.725   2.447
1UNL H6   13   2.241   2.628   2.315
1UNL H7   14   2.400   2.708   2.323
1UNL H8   15   2.565   2.244   2.568
1UNL LA   16   2.464   2.521   2.430
2HOH  O   17   2.592   2.475   2.796
2HOH  H   18   2.684   2.494   2.769
2HOH H1   19   2.589   2.419   2.716
2HOH H2   20   2.560   2.560   2.760
   5.0   5.0   5.0
**
link atom is placed between C1 and C2 atoms, whereas its coordinate was 
calculated by x2 = [(0.153*x1)+ (0.153*x3)]/(0.153+0.153)..


do you have an idea ?

Cheers




On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian <andrian.c...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi,

thank you for your kindly reply...

system has been successfully minimized, restrained NVT/NPT equilibrated, 
and unrestrained Classical MM before... there is no problem..


*
here is my equilibrated structure (strarting configuration for qmmm)
Grunge ROck MAChoS
   20
1UNL  C1   2.600   2.380   2.439
1UNL C12   2.540   2.521   2.421
1UNL  H3   2.554   2.304   2.376
1UNL  O4   2.587   2.339   2.575
1UNL H15   2.708   2.376   2.422
1UNL C26   2.388   2.522   2.440
1UNL H27   2.554   2.559   2.319
1UNL CL8   2.612   2.651   2.519
1UNL C39   2.327   2.649   2.379
1UNL H3   10   2.363   2.497   2.543
1UNL H4   11   2.354   2.441   2.375
1UNL H5   12   2.287   2.725   2.447
1UNL H6   13   2.241   2.628   2.315
1UNL H7   14   2.400   2.708   2.323
1UNL H8   15   2.565   2.244   2.568
1UNL LA   16   2.464   2.521   2.430
2HOH  O   17   2.592   2.475   2.796
2HOH  H   18   2.684   2.494   2.769
2HOH H1   19   2.589   2.419   2.716
2HOH H2   20   2.560   2.560   2.760
   5.0   5.0   5.0
**
link atom is placed between C1 and C2 atoms, whereas its coordinate was 
calculated by x2 = [(0.153*x1)+ (0.153*x3)]/(0.153+0.153)..


do you have an idea ?

Cheers



On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian <andrian.c...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol

[gmx-users] LINCS warning of QMMM simulation

[andrian]

ess
! XYZFile# Type of Coordinates

%scf
  SCFMode Direct
  MaxIter 1500
  UseCheapInts true
end
******



--
Andrian Saputra
Department of Pharmaceutical Science
Sumatera Institute of Technology, Indonesia

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