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Bug #3209

Interactive molecular dynamics with VMD becomes stuttering after reconnecting

Added by Christian Blau 17 days ago. Updated 17 days ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
mdrun
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

When using the IMD implementation in several versions of Gromacs including 2019.3 and different operating systems.

This bug occurs with the following steps:

- Run an IMD simulation (gmx mdrun -imdwait -imdpull -imdterm -s mysim.tpr)

- Connect to the simulation using VMD (or other visualization tool that implements the IMD protocol)

- Pause the simulation from VMD ("detach sim" button)

- Reconnect to the simulation

The expected behavior is to have the same performance before and after pausing the simulation.

The actual behavior is a slower and stuttering simulation. Note that this bug does not occur when using NAMD.

See an example of the bug here: https://www.youtube.com/watch?v=_gZ6wA7c4b8 <https://www.youtube.com/watch?v=_gZ6wA7c4b8&feature=youtu.be>

An error line appears in the gromacs window: "IMD: Failed to shutdown socket. Did the client already disconnect?" and "IMD: Error in file gromacs-2019.3/src/gromacs/imd/imdsocket.cpp on line 293."

topol.tpr (1.4 MB) topol.tpr testing IMD reconnection bug with a protein in water Xavier Martinez, 11/19/2019 11:35 AM

History

#1 Updated by Xavier Martinez 17 days ago

Thank you for filing this.

Here is a tpr file to start a simple IMD simulation with a protein in a water box.
This bug also occurs on gromacs 2018.3 on linux.

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