[Chimera-users] Imagine processing from gromacs

[benjamintam]

Hi Eric,

Thank you very much for your help. Although I am not sure whether is the university or the mailing list blocked the code content. Nevertheless, I appreciate your help.

Best regards,

Ben

Ph.D, M.Eng, FHEA

From: Eric Pettersen<mailto:pett at cgl.ucsf.edu>
Sent: 24 April 2020 02:51
To: benjamintam<mailto:benjamintam at um.edu.mo>
Cc: chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Imagine processing from gromacs

Hi Ben,
Typically, one "wraps" a PBC trajectory to produce a new trajectory where molecules stay whole on one side of the box or the other.  For Gromacs, the tool for that is trjconv, perhaps with the "-pbc whole" flags.  See this page: gmx trjconv - GROMACS 2018 documentation<https://urldefense.proofpoint.com/v2/url?u=http-3A__manual.gromacs.org_documentation_2018_onlinehelp_gmx-2Dtrjconv.html&d=DwMFaQ&c=KXXihdR8fRNGFkKiMQzstu-8MbOxd1NuZkcSBymGmgo&r=EElAJhvpEXZIOG4aO3Q_1Fg1wh-iIcDTLJ2t8QVMlxU&m=pJfYo02dBWyMImWhNt9SQhEshAF42kEnCABBWjH3NjM&s=Vfw1MLZfC1pHcWEsIFazzl3tZ-0l-fHmOMBi6IeaOBs&e=>.
If wrapping a trajectory is problematic for some reason, you could define a per-frame Python script to hide long bonds.  I have attached such a script.  To use it, in the MD Movie GUI choose the Per-Frame?Define script... menu entry, and in the resulting dialog change the script type to "Python" and use the "Insert text file" button near the button to insert the attached Python file.  Then click OK.  Long bonds should disappear and you can play your trajectory and bonds will be hidden and shown appropriately.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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