[gmx-users] How to use "gmx view" on Ubuntu?
Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Hi, You'll need to install X11 headers and libraries (the package is called xorg-dev, off the top of my head), and use cmake .. -DGMX_X11=on before compiling & installing. Mark On Tue, May 9, 2017 at 8:59 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. > > > When I run "gmx view ..." as below: > > > gmx view -f dppc-md.xtc -s dppc-md.tpr > > > I got the following: > > > Compiled without X-Windows - can not run viewer. > > > > > > Can I ask how to use "gmx view" on Ubuntu? Thank you. > > > Yours sincerely > Cheng > -- > 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] How to use "gmx view" on Ubuntu?
Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Hi, Just like all normal installations of GROMACS, you need to run cmake from your build directory and tell it where the source directory is. The ".." works if the source is the parent directory, but if you're not following eg the installation guide, then you'll have to adapt! Mark On Tue, 9 May 2017 22:23 ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs and Mark Abraham, > Sorry, I am not familiar with compiling issue. > > > I installed xorg-dev by: > sudo apt-get install xorg-dev > > > Then, I type > cmake .. -DGMX_X11=on > > > But I was told: > CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." > does not appear to contain CMakeLists.txt. > > > What I should do next? > > > Thank you. > > > Cheng > > > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, May 10, 2017 02:58 AM > To: "gromacs.org_gmx-users"; > > Subject: How to use "gmx view" on Ubuntu? > > > > Dear Gromacs, > I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. > > > When I run "gmx view ..." as below: > > > gmx view -f dppc-md.xtc -s dppc-md.tpr > > > I got the following: > > > Compiled without X-Windows - can not run viewer. > > > > > > Can I ask how to use "gmx view" on Ubuntu? Thank you. > > > Yours sincerely > Cheng > -- > 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] How to use "gmx view" on Ubuntu?
Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
On 5/10/17 11:27 AM, ZHANG Cheng wrote: Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) http://manual.gromacs.org/documentation/2016.3/download.html Then follow the installation instructions: http://manual.gromacs.org/documentation/2016.3/install-guide/index.html -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.
Re: [gmx-users] How to use "gmx view" on Ubuntu?
Dear Justin, Thank you for your link. I know how to install the Gromacs based on your link. But do you know where I can download the tar.gz file so that I can compile it and then use "gmx view"? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 11:27 PM To: "gromacs.org_gmx-users"; Subject: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Hi, Justin gave you a download link. Please try it. Mark On Wed, 10 May 2017 20:50 ZHANG Cheng <272699...@qq.com> wrote: > Dear Justin, > Thank you for your link. I know how to install the Gromacs based on your > link. But do you know where I can download the tar.gz file so that I can > compile it and then use "gmx view"? > > > Thank you. > > > Cheng > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, May 10, 2017 11:27 PM > To: "gromacs.org_gmx-users"; > > Subject: Re: Re: How to use "gmx view" on Ubuntu? > > > > Dear Mark Abraham, > Thank you very much for your updating. > > > Sorry, could you please tell me where can I download the cmake file, or > which command line to use, in order to compiling & installing? > > > I have tried the below and they both worked, but "gmx view …" still not > work, with the same issue "Compiled without X-Windows - can not run viewer." > ) sudo apt-get install xorg-dev > ) sudo apt-get install xorg-dev libglu1-mesa-dev > > > > (Sorry, I am not sure how to find the files to download) > > > Thank you. > > > Yours sincerely > Cheng > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, May 10, 2017 04:22 AM > To: "gromacs.org_gmx-users"; > > Subject: Re: How to use "gmx view" on Ubuntu? > > > > Dear Gromacs and Mark Abraham, > Sorry, I am not familiar with compiling issue. > > > I installed xorg-dev by: > sudo apt-get install xorg-dev > > > Then, I type > cmake .. -DGMX_X11=on > > > But I was told: > CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." > does not appear to contain CMakeLists.txt. > > > What I should do next? > > > Thank you. > > > Cheng > > > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, May 10, 2017 02:58 AM > To: "gromacs.org_gmx-users"; > > Subject: How to use "gmx view" on Ubuntu? > > > > Dear Gromacs, > I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. > > > When I run "gmx view ..." as below: > > > gmx view -f dppc-md.xtc -s dppc-md.tpr > > > I got the following: > > > Compiled without X-Windows - can not run viewer. > > > > > > Can I ask how to use "gmx view" on Ubuntu? Thank you. > > > Yours sincerely > Cheng > -- > 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] How to use "gmx view" on Ubuntu?
Dear Mark, Yes, Justin gave me a link for Gromacs-2016.3, but not the link for xorg-dev. Do you mean, I should uninstall my current Gromacs 5.0.4, then install the Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3 on my Ubuntu? Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 02:50 AM To: "gromacs.org_gmx-users"; Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? Dear Justin, Thank you for your link. I know how to install the Gromacs based on your link. But do you know where I can download the tar.gz file so that I can compile it and then use "gmx view"? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 11:27 PM To: "gromacs.org_gmx-users"; Subject: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
On 5/10/17 4:27 PM, ZHANG Cheng wrote: Dear Mark, Yes, Justin gave me a link for Gromacs-2016.3, but not the link for xorg-dev. Because you installed the necessary X11 components via apt-get. Do you mean, I should uninstall my current Gromacs 5.0.4, then install the Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3 on my Ubuntu? Yes. If you want any GROMACS version enabled with gmx view, you need the prerequisite X11 libraries and headers, and then you have to recompile GROMACS. -Justin Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 02:50 AM To: "gromacs.org_gmx-users"; Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? Dear Justin, Thank you for your link. I know how to install the Gromacs based on your link. But do you know where I can download the tar.gz file so that I can compile it and then use "gmx view"? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 11:27 PM To: "gromacs.org_gmx-users"; Subject: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- == 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.
Re: [gmx-users] How to use "gmx view" on Ubuntu?
Hi, On Wed, May 10, 2017 at 10:28 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Mark, > Yes, Justin gave me a link for Gromacs-2016.3, but not the link for > xorg-dev. > You don't need or want one. That's what the apt-get commands are for. > Do you mean, I should uninstall my current Gromacs 5.0.4, then install the > Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3 on > my Ubuntu? > You can install whatever version you want, but generally the latest version, or one with which you need scientific consistency are reasonable decisions. gmx view doesn't change much, though. As I said in my first reply you need to compile and install some new GROMACS version: "You'll need to install X11 headers and libraries (the package is called xorg-dev, off the top of my head), and use cmake .. -DGMX_X11=on before compiling & installing." Whether and how you need to uninstall your old GROMACS is dependent on it was previously installed. Generally there's no need to do so, but it might be a good idea. Mark Cheng > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Thu, May 11, 2017 02:50 AM > To: "gromacs.org_gmx-users"; > > Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? > > > > Dear Justin, > Thank you for your link. I know how to install the Gromacs based on your > link. But do you know where I can download the tar.gz file so that I can > compile it and then use "gmx view"? > > > Thank you. > > > Cheng > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, May 10, 2017 11:27 PM > To: "gromacs.org_gmx-users"; > > Subject: Re: Re: How to use "gmx view" on Ubuntu? > > > > Dear Mark Abraham, > Thank you very much for your updating. > > > Sorry, could you please tell me where can I download the cmake file, or > which command line to use, in order to compiling & installing? > > > I have tried the below and they both worked, but "gmx view …" still not > work, with the same issue "Compiled without X-Windows - can not run viewer." > ) sudo apt-get install xorg-dev > ) sudo apt-get install xorg-dev libglu1-mesa-dev > > > > (Sorry, I am not sure how to find the files to download) > > > Thank you. > > > Yours sincerely > Cheng > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, May 10, 2017 04:22 AM > To: "gromacs.org_gmx-users"; > > Subject: Re: How to use "gmx view" on Ubuntu? > > > > Dear Gromacs and Mark Abraham, > Sorry, I am not familiar with compiling issue. > > > I installed xorg-dev by: > sudo apt-get install xorg-dev > > > Then, I type > cmake .. -DGMX_X11=on > > > But I was told: > CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." > does not appear to contain CMakeLists.txt. > > > What I should do next? > > > Thank you. > > > Cheng > > > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, May 10, 2017 02:58 AM > To: "gromacs.org_gmx-users"; > > Subject: How to use "gmx view" on Ubuntu? > > > > Dear Gromacs, > I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. > > > When I run "gmx view ..." as below: > > > gmx view -f dppc-md.xtc -s dppc-md.tpr > > > I got the following: > > > Compiled without X-Windows - can not run viewer. > > > > > > Can I ask how to use "gmx view" on Ubuntu? Thank you. > > > Yours sincerely > Cheng > -- > 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] How to use "gmx view" on Ubuntu?
Hello Cheng, You can firstly install libX11-devel by yourself: # sudo apt-get install libx11-dev (in CentOS: sudo yum install libX11-devel) Then "cd build" and run: # cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_X11=on Thanks, Frank On 5/10/17, 2:33 PM, "Mark Abraham" wrote: >Hi, > >On Wed, May 10, 2017 at 10:28 PM ZHANG Cheng <272699...@qq.com> wrote: > >> Dear Mark, >> Yes, Justin gave me a link for Gromacs-2016.3, but not the link for >> xorg-dev. >> > >You don't need or want one. That's what the apt-get commands are for. > > >> Do you mean, I should uninstall my current Gromacs 5.0.4, then install >>the >> Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3 >>on >> my Ubuntu? >> > >You can install whatever version you want, but generally the latest >version, or one with which you need scientific consistency are reasonable >decisions. gmx view doesn't change much, though. > >As I said in my first reply you need to compile and install some new >GROMACS version: "You'll need to install X11 headers and libraries (the >package is called xorg-dev, off the top of my head), and use cmake .. >-DGMX_X11=on before compiling & installing." > >Whether and how you need to uninstall your old GROMACS is dependent on it >was previously installed. Generally there's no need to do so, but it might >be a good idea. > >Mark > >Cheng >> >> >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Thu, May 11, 2017 02:50 AM >> To: "gromacs.org_gmx-users"; >> >> Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? >> >> >> >> Dear Justin, >> Thank you for your link. I know how to install the Gromacs based on your >> link. But do you know where I can download the tar.gz file so that I can >> compile it and then use "gmx view"? >> >> >> Thank you. >> >> >> Cheng >> >> >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Wed, May 10, 2017 11:27 PM >> To: "gromacs.org_gmx-users"; >> >> Subject: Re: Re: How to use "gmx view" on Ubuntu? >> >> >> >> Dear Mark Abraham, >> Thank you very much for your updating. >> >> >> Sorry, could you please tell me where can I download the cmake file, or >> which command line to use, in order to compiling & installing? >> >> >> I have tried the below and they both worked, but "gmx view " still not >> work, with the same issue "Compiled without X-Windows - can not run >>viewer." >> ) sudo apt-get install xorg-dev >> ) sudo apt-get install xorg-dev libglu1-mesa-dev >> >> >> >> (Sorry, I am not sure how to find the files to download) >> >> >> Thank you. >> >> >> Yours sincerely >> Cheng >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Wed, May 10, 2017 04:22 AM >> To: "gromacs.org_gmx-users"; >> >> Subject: Re: How to use "gmx view" on Ubuntu? >> >> >> >> Dear Gromacs and Mark Abraham, >> Sorry, I am not familiar with compiling issue. >> >> >> I installed xorg-dev by: >> sudo apt-get install xorg-dev >> >> >> Then, I type >> cmake .. -DGMX_X11=on >> >> >> But I was told: >> CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... >>..." >> does not appear to contain CMakeLists.txt. >> >> >> What I should do next? >> >> >> Thank you. >> >> >> Cheng >> >> >> >> >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Wed, May 10, 2017 02:58 AM >> To: "gromacs.org_gmx-users"; >> >> Subject: How to use "gmx view" on Ubuntu? >> >> >> >> Dear Gromacs, >> I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. >> >> >> When I run "gmx view ..." as below: >> >> >> gmx view -f dppc-md.xtc -s dppc-md.tpr >> >> >> I got the following: >> >> >> Compiled without X-Windows - can not run viewer. >> >> >> >> >> >> Can I ask how to use "gmx view" on Ubuntu? Thank you. >> >> >> Yours sincerely >> Cheng >> -- >> 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/g
Re: [gmx-users] How to use "gmx view" on Ubuntu?
Dear Justin, Mark and Frank, Thank you so much for explaining it. Now I think I understand it. I was confusing because I thought, I should install/compile the xorg-dev by using "cmake". But actually, what you meant is, use "cmake" to compile Gromacs after installing xorg-dev. I tried as Frank suggested for the cmake command line, including "-DGMX_X11=on", using my original Gromacs 5.0.4 files. But some problems occurred on the cmake. But I managed to use VMD to visualise my xtc file. So it is okay for me now. Thank you for all your help! Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 04:27 AM To: "gromacs.org_gmx-users"; Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark, Yes, Justin gave me a link for Gromacs-2016.3, but not the link for xorg-dev. Do you mean, I should uninstall my current Gromacs 5.0.4, then install the Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3 on my Ubuntu? Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 02:50 AM To: "gromacs.org_gmx-users"; Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? Dear Justin, Thank you for your link. I know how to install the Gromacs based on your link. But do you know where I can download the tar.gz file so that I can compile it and then use "gmx view"? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 11:27 PM To: "gromacs.org_gmx-users"; Subject: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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.
