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
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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric, 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. Thank you! Alan ________________________________ 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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Alan, The Join Models section of Build Structure will work if you have the two parts (protein and thioester molecule) opened as two separate models, i.e. each was opened from a different file. Of course, you have to use the "other bond" option because it is not a peptide bond. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join> If they are already in the same model as each other, then you can just add a bond between atoms using the Adjust Bonds section of Build Structure... however this will not move the two parts relative to each other, it will just add the bond in their current positions. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2023, at 12:07 PM, Alan Carbajo via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Eric,
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.
Thank you!
Alan
participants (3)
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Alan Carbajo -
Elaine Meng -
Eric Pettersen