Dear Sir,
I have found in literature that most of the unfolding studies of proteins are performed at higher temperature by increasing box size accordingly. My protein has approximately 70 residues, & I want to simulate it at room temperature as well as at some higher temperatures. I have not increased box size at higher temperatures in order to avoid computational cost, as right now we have some space problem. All my protein atoms are at a distance equal to 1.0 nm from the box edges at all temperatures. I have three queries. 1) Will the result be erroneous if I keep box size unaltered at higher temperature? 2) What should be minimum distance between protein atoms and box edges? I have found that some authors say minimum distance will be 0.85 nm, but I also have found that several authors carried on simulations with dist 0.5nm between protein atoms and box edges, so I am getting confused. 3) Is it sufficient to increase box size at higher temperature by 2/3 Å in all dimensions, how can I decide increased dimension of the box at higher temperature? Please help. Thanking you in advance. regards Sangeeta |
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