VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 16 2021 - 11:48:14 CDT

Hi,
  A quick follow up: The new VMD test builds for Catalina+Big Sur DO contain
the Gromacs plugins, so I would expect them to operate normally. If someone
identifies cases that do not work as expected, please call our attention to them.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 16, 2021 at 03:54:00PM +0000, Chang, Christopher wrote:
> Hi Davide,
>
>
>
> Do you see the atoms moving with another visualization approach
> ([1]https://manual.gromacs.org/current/how-to/visualize.html)? That would
> narrow down whether it was a VMD issue, or a problem with the trajectory
> file input. A handful of frames is probably enough for a test case.
>
>
>
> Cheers; Chris
>
>
>
> From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of alberto
> <voodoo.bender_at_gmail.com>
> Date: Tuesday, March 16, 2021 at 7:25 AM
> To: Davide Marchi <davide.marchi_at_uniupo.it>
> Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: cannot visualize GROMACS trajectories in VMD 1.9.4 on
> MacOS Big Sur
>
>
>
> CAUTION: This email originated from outside of NREL. Do not click links or
> open attachments unless you recognize the sender and know the content is
> safe.
>
> Hi,
>
> there is no reason why some atoms do not move in fact as you point out no
> error message appears in the vmd console. i think there is an error in the
> gromacs dynamics. perhaps you are not a skilled user of this calculation
> method.
>
>
>
> Al
>
>
>
> Il giorno mar 16 mar 2021 alle 12:20 Davide Marchi
> <[2]davide.marchi_at_uniupo.it> ha scritto:
>
> dear VMD users,
>
> my OS is macOS Big Sur version 11.2.1 and i'm using VMD version 1.9.4
> when i load a GROMACS .trr trajectory i don't see any error messages,
> but the atoms won't move. the same trajectory files behave as expected
> when loaded on a different machine and VMD version (Windows 7 virtual
> environment with VMD 1.9.3).
>
> are GROMACS trajectories still not implemented in VMD 1.9.4 for mac?
> thanks in advance.
>
> References
>
> Visible links
> 1. https://urldefense.com/v3/__https://manual.gromacs.org/current/how-to/visualize.html__;!!DZ3fjg!r4x1p7_05tPeWJkDhjbZOf6m7H7XvuYhmfJhOis4W-UZXTUlxgTe5-7IGQhzMP71zw$
> 2. mailto:davide.marchi_at_uniupo.it 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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