Dear gmxuser I want to analyze the secondary structure of a protein after a 10ns simulation run but I do not know how long it will take because I run it for more than 2 hours but it is still running.I don't know whether I am encountering any problem , in the manual it is mentioned that the program is very slow. But it is not mention how long. I saw in gmx mailing list that somebody has my problem before but his problem solved by my_dssp. Unfortunately, I could not also run my_dssp and I faced with many error.
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