VMD-L Mailing List

From: Chang, Christopher (Christopher.Chang_at_nrel.gov)
Date: Tue Mar 16 2021 - 10:54:00 CDT

Hi Davide,

   Do you see the atoms moving with another visualization approach (https://urldefense.com/v3/__https://manual.gromacs.org/current/how-to/visualize.html)?__;!!DZ3fjg!r4x1p7_05tPeWJkDhjbZOf6m7H7XvuYhmfJhOis4W-UZXTUlxgTe5-7IGQhOElUV-g$ 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

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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 <davide.marchi_at_uniupo.it<mailto: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.