Hi Chris, The two setups were different from each other in terms of only the number of water molecules. Even the starting conformations for the two peptides were the same. I especially took care about that to leave only the number of molecules as a variable.
I calculated the error by dividing the whole data to 4, and calculated the standard deviation between the 4 sets, and divided the result by sqrt (3). For the Xavier's suggestion: I think I should wait a little, at least until having the same length of trajectory for the two sets. Thanks -- Ozge Engin ★☆
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