[gmx-users] How to use "gmx view" on Ubuntu?

[Mark Abraham]

Hi,

On Wed, May 10, 2017 at 10:28 PM ZHANG Cheng <272699575 at 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";<272699575 at qq.com>;
> Date:  Thu, May 11, 2017 02:50 AM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> 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";<272699575 at qq.com>;
> Date:  Wed, May 10, 2017 11:27 PM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> 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";<272699575 at qq.com>;
> Date:  Wed, May 10, 2017 04:22 AM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> 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";<272699575 at qq.com>;
> Date:  Wed, May 10, 2017 02:58 AM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> 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-request at gromacs.org.