Temperature during chimera minimization (pdb)
Dear Chimera user
I have calculated the structures of a peptide at 273K (0 °C), then I have extracted low energy structures and minimization them in chimera. I am not sure chimera performed minimization at 273K or 298K. Could any one suggest me at what temperature chimera performs minimization (with explicit solvent), is there is a way to set different temperature.
thank you so much in advance...
Vince
Dear Vince, Minimization does not use a temperature. In molecular dynamics there is a concept of temperature from the kinetic energy put into the system, but this is not done in minimization. Sometimes the minimized state is described as “zero Kelvin,” but that may be an oversimplification. It only depends on the force field parameters and force field equation. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 29, 2016, at 7:06 AM, Vasantha Kumar vin.vasanth@gmail.com wrote:
Dear Chimera user
I have calculated the structures of a peptide at 273K (0 °C), then I have extracted low energy structures and minimization them in chimera. I am not sure chimera performed minimization at 273K or 298K. Could any one suggest me at what temperature chimera performs minimization (with explicit solvent), is there is a way to set different temperature.
thank you so much in advance...
Vince
Dear Elaine,
Thank you so much for your quick response. Your answer cleared my doubt.
Again, thanks a lot.
Have a good day…
With best wishes Vince
On 29-Feb-2016, at 6:07 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Vince, Minimization does not use a temperature. In molecular dynamics there is a concept of temperature from the kinetic energy put into the system, but this is not done in minimization. Sometimes the minimized state is described as “zero Kelvin,” but that may be an oversimplification. It only depends on the force field parameters and force field equation. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 29, 2016, at 7:06 AM, Vasantha Kumar vin.vasanth@gmail.com wrote:
Dear Chimera user
I have calculated the structures of a peptide at 273K (0 °C), then I have extracted low energy structures and minimization them in chimera. I am not sure chimera performed minimization at 273K or 298K. Could any one suggest me at what temperature chimera performs minimization (with explicit solvent), is there is a way to set different temperature.
thank you so much in advance...
Vince
participants (3)
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Elaine Meng -
Vasantha Kumar -
Vasantha Kumar M. V.