Dear modellers, I did optimization for my modelled protein using molecular dynamics "OPTIMIZATION_METHOD = 3". If I decrease the temperature from 300(modeller default value )to lower temperatue (eg., 200K,100K) the total energy of the optimized model decreases ,if I increase the temperature from 300 to higher temperature (eg., 400,500)the total energy of optimized model also increases. I do aware of that as the energy minimizes ,the model approaching its native nate or perfection. My question now is 1) wheather this behaviour happens with all protein (I mean increasing energy with initial temperature and vivevarsa)? 2) What are the useful conclution that I can derive out of this behaviour of my modeled protein ?
Looking forward keenly to hear something from you. Yours truly, B.Nataraj
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