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Thread: vmd problems

  1. #1
    Join Date
    Sep 2008
    Beans
    11

    vmd problems

    Hi,

    I very recently installed ubuntu 8.04 and am now trying to run vmd (visual molecular dynamics), but am having the following problem: the molecular display window flashes on mouse-over but disappears otherwise, and is generally unusable. Also, the window title bar and scroll bar are invisible, but still exist - I can minimize/maximize the window by clicking where the appropriate buttons should be.

    I don't know if this is at all related to the above problem, but the following two statements appear in the vmd console window:

    Info) ATI Linux driver detected, limiting features to avoid driver bugs.
    .
    .
    .
    Info) GLSL rendering mode is NOT available.

    Here is my setup:

    AMD Athlon64
    ATI MSI Radeon X300 SE
    BENQ T701 lcd monitor (if this makes any difference)


    I've installed the newest ATI linux x64 driver from their page, but it doesn't seem to make a difference.

    Please help!
    Last edited by rvs070; October 3rd, 2008 at 07:53 AM.

  2. #2
    Join Date
    Oct 2006
    Beans
    20

    Re: vmd problems

    Hi:

    Clients of mine who work in our Chemistry department are suffering the same issue. I thought maybe that it has something to do with the fact that we are using Intel's G35 integrated graphics chip.

    I have the problem on both 8.04.1 and 8.10 (64-bit). I am going to try and compile the program from the source code and see what happens. (Although I expect the results to be exactly the same). I read through the Linux release notes documentation but found nothing there which could help me.

    Did you join the vmd mailing list? I haven't yet, but I would like to post the same question there.

    This is my output via the vmd console:

    Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
    Info) http://www.ks.uiuc.edu/Research/vmd/
    Info) Email questions and bug reports to vmd@ks.uiuc.edu
    Info) Please include this reference in published work using VMD:
    Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
    Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
    Info) -------------------------------------------------------------
    Info) Multithreading available, 2 CPUs detected.
    Info) Free system memory: 3367MB (85%)
    Info) OpenGL renderer: Mesa DRI Intel(R) 965G 20061102
    Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
    Info) Full GLSL rendering mode is available.
    Info) Textures: 2-D (2048x2048), 3-D (256x256x256), Multitexture (8)
    vmd >

    Otherwise, I suffer the same issues you do:
    - invisible scroll bar and windows frame widgets
    - screen flickers and gets in the way of all other windows

    Any help would be greatly appreciated.

  3. #3
    Join Date
    May 2009
    Beans
    2

    Re: vmd problems

    Hello I have exactly the same problems with vmd 1.8.6 and Ubuntu 9.04.
    Does anyone has an update?

    Thanks

  4. #4
    Join Date
    Feb 2006
    Location
    Vancouver
    Beans
    53
    Distro
    Ubuntu 9.04 Jaunty Jackalope

    Re: vmd problems

    For me this is a conflict with the desktop effects.

    Try disabling them by going to Appearance --> Visual Effects tab and setting it to 'none', then start VMD.

    It's too bad because some of the other UI features I want to use (AWN, Gnome-DO) are much better to use with these effects enabled.

  5. #5
    Join Date
    Dec 2008
    Beans
    7

    Re: vmd problems

    Quote Originally Posted by Bionic_Beefpile View Post
    For me this is a conflict with the desktop effects.

    Try disabling them by going to Appearance --> Visual Effects tab and setting it to 'none', then start VMD.
    That solved this issue for me. Thanks!

  6. #6
    Join Date
    Oct 2010
    Beans
    5

    Re: vmd problems

    Hi!

    Same problem here. Ubuntu 10.04, vmd 1.8.7 and Radeon 5730 with ati catalyst 10.09.

    Disabling Visual Effects tip works, but it's too bad....


    Thanks

  7. #7
    Join Date
    Oct 2010
    Beans
    1

    Re: vmd problems

    Thank you!

  8. #8
    Join Date
    Oct 2010
    Beans
    5

    Re: vmd problems

    I Everyone!

    I think i have found a way to workaround this problem... I just added the this entry to my .bashrc:

    unset LIBGL_ALWAYS_INDIRECT

    and now i can run VMD with compiz!

    (I'm runing Ubuntu 10.10 64bits)

    Hope this helps,
    André
    Last edited by andre_f; December 29th, 2010 at 01:05 PM.

  9. #9
    Join Date
    Sep 2006
    Beans
    1,188
    Distro
    Ubuntu 10.10 Maverick Meerkat

    Re: vmd problems

    Hello,

    I had exactly the same problem, yet while connected remotely to another computer. Compiz enabled. With catalyst 11.10 for ubuntu maverick, this flickering thing is almost gone. For my desktop use I do not remember facing such an issue.

    EDIT:I was able to check that the problem remained with tear free option enabled. As a result this version of driver might not be a solution. With tear free on, flash videos are ok, yet the vmd screen flickers all the time. With tear free off, things are looking nice for vmd. Always this for remote connection.

    Regards!
    Last edited by Claus7; November 3rd, 2011 at 01:01 AM. Reason: adding info

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