Thank you for the reply. A follow up question, I have a protein with a CYS whose sulfur forms a thioester and a carbon chain. I have a pdb for the large protein, and the separate thioester molecule that forms. Is it possible to replace the current S on the CYS and join it with the new one? I noticed the join molecule button doesn't work for it and the only thing I can do is build it using the add button.

From: Eric Pettersen <pett@cgl.ucsf.edu>
Sent: Thursday, May 4, 2023 1:50 PM
To: Alan Carbajo <ga5808@wayne.edu>
Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] UCSF Chimera Molecular Dynamics: CPU vs GPU

[EXTERNAL]

Hi Alan,

The MMTK toolkit, which Chimera uses for MD calculations, does not support GPU acceleration. However, it does allow the use of multiple CPUs, which most modern machines have. To use multiple CPUs go to the Molecular Dynamics Simulation “Run Parameters” tab and change “Settings” to “other runtime options” and check the “Use multiple CPUs” box.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On May 4, 2023, at 8:48 AM, Alan Carbajo via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Good morning,

I'm running a molecular dynamics simulation in Chimera, and it seems that the program is only using my cpu for the calculations. Why is this? Is it possible to switch it to use my GPU?

Thank you,

Alan

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