Search found 3 matches

by starless
Thu Oct 20, 2011 11:57 am
Forum: Running simulations
Topic: rattle: too many constraint iterations.
Replies: 7
Views: 12288

Re: rattle: too many constraint iterations.

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 ...
by starless
Thu Oct 06, 2011 4:42 pm
Forum: Running simulations
Topic: rattle: too many constraint iterations.
Replies: 7
Views: 12288

Re: rattle: too many constraint iterations.

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...
by starless
Mon Oct 03, 2011 1:37 pm
Forum: Running simulations
Topic: rattle: too many constraint iterations.
Replies: 7
Views: 12288

Re: rattle: too many constraint iterations.

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).