Re: [gmx-users] ZnO Parameters
https://elib.suub.uni-bremen.de/edocs/00104076-1.pdf Page 111. On Tue, Jul 10, 2018 at 7:38 AM, wrote: > > Message: 3 > > Date: Fri, 6 Jul 2018 14:39:15 +0300 > > From: ali akg?n > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] ZnO Parameters > > Message-ID: > >hkwchrutet...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Hi, > > > > You can f?nd parameters on solid state books(for example kittel) > > Thank you for your kind suggestion. However I didn't found much info from > it. > > > > > Thank you. > > > > > > 6 Tem 2018 Cum 13:09 tarihinde ?unu yazd?: > > > >> Dear Gromacs Users > >> > >> Can anyone provide me the parameters for Zinc Oxide (ZnO)? > >> > >> Thank You > >> > >> Regards > >> Zaved Hazarika > >> PhD Scholar > >> Dept.of Molecular Biology and Biotechnology > >> Tezpur University > >> India > > Thank You > > Regards > Zaved > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > 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.
Re: [gmx-users] ZnO Parameters
Hi, You can fınd parameters on solid state books(for example kittel) Thank you. 6 Tem 2018 Cum 13:09 tarihinde şunu yazdı: > Dear Gromacs Users > > Can anyone provide me the parameters for Zinc Oxide (ZnO)? > > Thank You > > Regards > Zaved Hazarika > PhD Scholar > Dept.of Molecular Biology and Biotechnology > Tezpur University > India > > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > 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.
[gmx-users] Generate unit cell
Hello, I have an polymer pdb file, I want to generate crystal unit structure of the pdb file. How can I generate unit cell structure of molecular systems ? Thank you. -- 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.
Re: [gmx-users] Installation error
Should i use another version of cmake ? On Sat, Mar 24, 2018 at 3:05 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > If you have fftw 3.3.7, then you don't need to ask the GROMACS build system > to download and build fftw for you. The error is suggesting that the issue > is that your CMake build wasn't configured to be able to do the download > that your asking GROMACS to ask CMake to do. > > Mark > > On Sat, Mar 24, 2018, 12:28 ali akgün <ali.akgunp...@gmail.com> wrote: > > > Hello, > > > > I got an error in gromacs-5.0.7 installiation cmake part. > > > > My error is: > > > > > > Scanning dependencies of target fftwBuild > > Scanning dependencies of target mdrun_objlib > > Scanning dependencies of target view_objlib > > [ 0%] Performing pre-download step for 'fftwBuild' > > [ 0%] Creating directories for 'fftwBuild' > > -- downloading... > > src='http://www.fftw.org/fftw-3.3.3.tar.gz' > > > > dest='/home/ali/Downloads/gromacs-5.0.7/build/src/ > contrib/fftw/fftw.tar.gz' > > CMake Error at fftw-download.cmake:9 (file): > > file DOWNLOAD not supported by bootstrap cmake. > > > > > > src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for > target > > > > 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/ > fftwBuild-pre-download' > > failed > > make[2]: *** > > > > [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/ > fftwBuild-pre-download] > > Error 1 > > make[2]: *** Waiting for unfinished jobs > > CMakeFiles/Makefile2:1124: recipe for target > > 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed > > make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2 > > make[1]: *** Waiting for unfinished jobs > > [ 1%] Building CXX object > > src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o > > [ 1%] Built target view_objlib > > [ 1%] Building C object > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o > > [ 2%] Building C object > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o > > [ 2%] Building C object > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o > > [ 2%] Building C object > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o > > [ 2%] Building CXX object > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o > > [ 2%] Building C object > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o > > [ 2%] Built target mdrun_objlib > > Makefile:162: recipe for target 'all' failed > > make: *** [all] Error 2 > > > > > > How to fix this error? > > > > Cmake version is 3.11.0 > > FFTW version is 3.3.7 > > > > Thank you. > > -- > > 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. -- 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.
[gmx-users] Installation error
Hello, I got an error in gromacs-5.0.7 installiation cmake part. My error is: Scanning dependencies of target fftwBuild Scanning dependencies of target mdrun_objlib Scanning dependencies of target view_objlib [ 0%] Performing pre-download step for 'fftwBuild' [ 0%] Creating directories for 'fftwBuild' -- downloading... src='http://www.fftw.org/fftw-3.3.3.tar.gz' dest='/home/ali/Downloads/gromacs-5.0.7/build/src/contrib/fftw/fftw.tar.gz' CMake Error at fftw-download.cmake:9 (file): file DOWNLOAD not supported by bootstrap cmake. src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for target 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-pre-download' failed make[2]: *** [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-pre-download] Error 1 make[2]: *** Waiting for unfinished jobs CMakeFiles/Makefile2:1124: recipe for target 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs [ 1%] Building CXX object src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o [ 1%] Built target view_objlib [ 1%] Building C object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o [ 2%] Building C object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o [ 2%] Building C object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o [ 2%] Building C object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o [ 2%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o [ 2%] Building C object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o [ 2%] Built target mdrun_objlib Makefile:162: recipe for target 'all' failed make: *** [all] Error 2 How to fix this error? Cmake version is 3.11.0 FFTW version is 3.3.7 Thank you. -- 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.
[gmx-users] installation error
Hello, I got an error in gromacs-5.1.5 installiation cmake part. My error is: *** glibc detected *** cmake: free(): invalid pointer: 0x009f241d *** How to fix this error? Thank you. -- 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.
[gmx-users] gmx dipole and gmx potential
Hİ all I am newbie and GROMACS, I did some dipole moment and electric potential calculation for water solutions. I want to understand gmx dipole and gmx potential algorithm.I read GROMACS manual 8.5.4 and 8.5.3 but I can not understand about gmx dipole algorithm, so I need information about gmx dipole algorithm. Thank you. -- 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.
[gmx-users] Pressure through one direction
Hi, Can i generate mdp file for pressure through one direction system.For example: Ref pressure: X direction:1.0 bar Other direction: 0.0 bar Thank you. -- 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.
Re: [gmx-users] Build thin film.
Thank you :) On Sun, Nov 26, 2017 at 11:36 PM, Dallas Warren <dallas.war...@monash.edu> wrote: > You can do whatever you want, and there are many tools to help you do that. > > Couple of options are using gmx insert-molecules (constrain the box > size to make the film, then enlarge afterwards to insert other > molecules), gmx genconf (just stack as required, some initial care > with runs will be required to get to correct size/density), or packmol > (http://www.ime.unicamp.br/~martinez/packmol/home.shtml) > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 24 November 2017 at 03:51, ali akgün <ali.akgunp...@gmail.com> wrote: > > I have a pdb file can i build thin film ? > > -- > > 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. -- 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.
[gmx-users] Build thin film.
I have a pdb file can i build thin film ? -- 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.
Re: [gmx-users] Pressure Fluactiation
I will run with bigger nsteps (like monte carlo :D) , thank you for reply sir. On Wed, Nov 22, 2017 at 11:17 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Yes, by running longer, or on a larger system, just as statistical > mechanics predicts. > > Mark > > On Wed, Nov 22, 2017 at 10:16 PM ali akgün <ali.akgunp...@gmail.com> > wrote: > > > Hİ, > > Thank you for reply but can i minimize fluctuation? > > > > On Wed, Nov 22, 2017 at 11:05 PM, Mark Abraham <mark.j.abra...@gmail.com > > > > wrote: > > > > > Hi, > > > > > > It's hard to say anything in the absence of any numbers about average > or > > > fluctuations. Do check out > > > http://www.gromacs.org/Documentation/Terminology/Pressure > > > > > > Mark > > > > > > On Wed, Nov 22, 2017 at 9:59 PM ali akgün <ali.akgunp...@gmail.com> > > wrote: > > > > > > > Hİ all, > > > > > > > > I ran simulation of pvdf(ligand) in solution. My problem is pressure > > > > fluctuation, My system's pressure fluctuated around reference > pressure > > > and > > > > average pressure is not equal to my reference pressure. I did well > > > > minimisation and nvt run for system before npt run. What should i do > > > about > > > > average pressure and reference pressure non-equality? I want to > control > > > > system pressure because I research about pressure depended potential > > > across > > > > the box behavour of the pvdf. > > > > > > > > Thank you. > > > > -- > > > > 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. > > -- > > 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. > -- 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.
Re: [gmx-users] Pressure Fluactiation
Hİ, Thank you for reply but can i minimize fluctuation? On Wed, Nov 22, 2017 at 11:05 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > It's hard to say anything in the absence of any numbers about average or > fluctuations. Do check out > http://www.gromacs.org/Documentation/Terminology/Pressure > > Mark > > On Wed, Nov 22, 2017 at 9:59 PM ali akgün <ali.akgunp...@gmail.com> wrote: > > > Hİ all, > > > > I ran simulation of pvdf(ligand) in solution. My problem is pressure > > fluctuation, My system's pressure fluctuated around reference pressure > and > > average pressure is not equal to my reference pressure. I did well > > minimisation and nvt run for system before npt run. What should i do > about > > average pressure and reference pressure non-equality? I want to control > > system pressure because I research about pressure depended potential > across > > the box behavour of the pvdf. > > > > Thank you. > > -- > > 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. -- 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.
[gmx-users] Pressure Fluactiation
Hİ all, I ran simulation of pvdf(ligand) in solution. My problem is pressure fluctuation, My system's pressure fluctuated around reference pressure and average pressure is not equal to my reference pressure. I did well minimisation and nvt run for system before npt run. What should i do about average pressure and reference pressure non-equality? I want to control system pressure because I research about pressure depended potential across the box behavour of the pvdf. Thank you. -- 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.
[gmx-users] Pİezoelectricity analyse
Hi, İ am newbie in Gromacs i processed pvdf(polymer) simulation in Gromacs for analyze piezoelectricity effect of pvdf in the different pressure and temperature.(using gmx dipole) Can i process different methods for analyze piezoelectric effect of pvdf. İ only know analyze dipole moments of system. Do you know another methods in gromacs ? Thank you. -- 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.
