[gmx-users] Drude polarization ff for Ca2+ and Mg2+
Dear GMX users, I am wondering where I can find the polarization parameter for Ca2+ and/or Mg2+ for Gromacs? Best, Xianchi -- 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] Drude force field
I simply put the ff files to the working folder and used the previous installed Gromacs 5.1.2. When use pdb2gmx, it gives the error msg: Fatal error: in .rtp file in residue anisotropic_polarization at line: DO1O1C1 LP1A LP1B 0.8108 1.2162 0.9730 Could you give me some advise? Best, Xianchi On Fri, Oct 28, 2016 at 3:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/28/16 2:48 PM, Xianchi Dong wrote: > >> Thanks for your reply. >> Do I need to copy the ff file to any folder? >> >> > Either the working directory or $GMXLIB, like any other force field. > > -Justin > > > Best, >> Xianchi >> >> On Oct 28, 2016, at 1:56 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 10/28/16 1:39 PM, Xianchi Dong wrote: >>>> Dear all, >>>> Does anyone have a detailed protocol to install Drude polarized force >>>> field on Gromacs? >>>> >>>> >>> There's nothing special about installation or use: >>> >>> http://mackerell.umaryland.edu/charmm_drude_ff.shtml >>> >>> Be aware that runs using domain decomposition may crash due to an as-yet >>> unresolved bug. I'm working on it, but it's below certain other priorities >>> at the moment. OpenMP runs are fine. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> 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. >>> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] Drude force field
Thanks for your reply. Do I need to copy the ff file to any folder? Best, Xianchi > On Oct 28, 2016, at 1:56 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> On 10/28/16 1:39 PM, Xianchi Dong wrote: >> Dear all, >> Does anyone have a detailed protocol to install Drude polarized force field >> on Gromacs? >> > > There's nothing special about installation or use: > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > Be aware that runs using domain decomposition may crash due to an as-yet > unresolved bug. I'm working on it, but it's below certain other priorities > at the moment. OpenMP runs are fine. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] Drude force field
Dear all, Does anyone have a detailed protocol to install Drude polarized force field on Gromacs? Best, Xianchi -- 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] QMMM install on GMX5.1 (Xianchi Dong)
Hi Andrew, Thanks for reply I tried to configure with cmake, the command I used is cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_PREFIX_PATH=../../mopac_lib/ -DCMAKE_INSTALL_PREFIX=~/Programs/Gromacs-5.1.2/ -DGMX_QMMM_MOPAC=on When I used make. It prompted with error msg: Linking CXX executable ../../bin/template ../../lib/libgromacs.so.1.2.0: undefined reference to `domop_' ../../lib/libgromacs.so.1.2.0: undefined reference to `domldt_' collect2: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 Best, Xianchi On Sun, Oct 16, 2016 at 8:37 PM, Andrew Guy <andrew@burnet.edu.au> wrote: > Hi Xianchi, > > It would be more helpful if you can provide a detailed description of what > failed when you tried to install QMMM. Just saying it failed doesn't give > people much insight into how to assist you. > > There are a myriad of possibilities, but without an actual error message to > go off, we're all in the dark here. > > Regards, > > Andrew > > On Mon, Oct 17, 2016 at 11:20 AM, Xianchi Dong <dongxian...@gmail.com> > wrote: > > > Hi Clinton, > > Thanks a lot for your reply. I tried but still failed. > > Would you like to say more about how to configure Gromacs 5.1.2 with > > CPPFLAGS, LIBS, and LDGFLAGS with cmake. > > > > Best, > > Xianchi > > > > > > > On Oct 15, 2016, at 12:52 PM, Clinton King <clintonkin...@chem.byu.edu > > > > wrote: > > > > > > Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html > > > > > > You will also need to set the following variable at install time: > > > > > > -DGMX_QMMM_MOPAC=ON > > > > > > -- > > > Clinton King > > > Graduate Student > > > Chemistry Department > > > Brigham Young University > > > > > > > > >> > > >> 1. QMMM install on GMX5.1 (Xianchi Dong) > > >> > > >> > > >> Message: 1 > > >> Date: Fri, 14 Oct 2016 17:14:36 -0400 > > >> From: Xianchi Dong <dongxian...@gmail.com> > > >> To: gromacs.org_gmx-users@maillist.sys.kth.se > > >> Subject: [gmx-users] QMMM install on GMX5.1 > > >> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com> > > >> Content-Type: text/plain; charset=us-ascii > > >> > > >> Hi all, > > >> Does anyone know how to install qmmm code like mopac to gmx5.1? > > >> > > >> Best, > > >> Xianchi > > >> > > >> > > >> > > > -- > > > 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] QMMM install on GMX5.1 (Xianchi Dong)
Hi Clinton, Thanks a lot for your reply. I tried but still failed. Would you like to say more about how to configure Gromacs 5.1.2 with CPPFLAGS, LIBS, and LDGFLAGS with cmake. Best, Xianchi > On Oct 15, 2016, at 12:52 PM, Clinton King <clintonkin...@chem.byu.edu> wrote: > > Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html > > You will also need to set the following variable at install time: > > -DGMX_QMMM_MOPAC=ON > > -- > Clinton King > Graduate Student > Chemistry Department > Brigham Young University > > >> >> 1. QMMM install on GMX5.1 (Xianchi Dong) >> >> >> Message: 1 >> Date: Fri, 14 Oct 2016 17:14:36 -0400 >> From: Xianchi Dong <dongxian...@gmail.com> >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] QMMM install on GMX5.1 >> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com> >> Content-Type: text/plain; charset=us-ascii >> >> Hi all, >> Does anyone know how to install qmmm code like mopac to gmx5.1? >> >> Best, >> Xianchi >> >> >> > -- > 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] QMMM install on GMX5.1
Hi all, Does anyone know how to install qmmm code like mopac to gmx5.1? Best, Xianchi -- 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.
