biowerkzeug

Hi Martin, It seems that transrot scan with default parameters is totally wrong: it gives the global minimum with z = -60 and helices parallel to the membrane. I don't really understand the difference between the tilt and twist, but I definitely know that my helices must be parallel to the membrane ...

Hi Martin, Thank you for the reply. If GBIM is implemented only for MC, what will I get if I run MD with IM turned on? Do you have a protein or a peptide? I have a large protein with extracellular domain, helices parallel to membrane and TM helices. I know that TM helices are perpendicular to the me...

And what should I do if I get this error when I want to make a GBIM MD simulation? Without rattle it's rather slow (1 step/s).