[gmx-users] Energy Miinimization question

[Vytautas Rakeviius]

As you set smaller emtol you do better and longer minimization. So with 1000 you stop simulation way before polymer forms some rings. You can check video with VMD Chimera or something.
 

    On Saturday, April 1, 2017 8:25 PM, Mishelle Oña <samimishu at hotmail.com> wrote:
 

 Hello everybody,

I have a question about the final conformation after energy minimization. I am simulating a polymer in vacuo and I used steepest descent method for energy minimization. When I use an emtol=1000 the structure I get is linear. Then I tried an emtol=30 because another study about the same polymer used this value but the final structure has some rings, I am not sure why this happened.

Thanks for your help.

Mishelle
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