biowerkzeug

In protein folding proteins can get stuck for very long times. In particular if the sequence has a lot of charged sidechains and the temperature is too low. I am seeing similar behaviour at the moment with a peptide that is now at 2 billion MC steps and still not folded propertly.

Using a very hydrophobic sequence shows that the program runs fine.

There are several options you could try:
1. Higher temperature (e.g. 350K or 400K) or
2. Replica exchange (REMC), say 20 replicas from 300-500K. The latter worked very well for our systems but you can also try a broader range if your system is very stuck: 300-600K.

You can run REMC on one processor in principle (it's slow though). It generally greatly speeds up the sampling.

Sorry i can't help any better, but trapped states is a very common problem in protein folding, most of our simulations took many trials and months to run.

Good luck!!

Best wishes,
Martin

Hello Martin,
thx for your reply at first. In my case the protein is a highly charged one and if you say this is causing the trouble, I am ok with it. So I will run my simulations for a much longer time and I will try the replica exchange method.
After this is done, I will tell you if and how it worked out.
Thx for all your support.
Your m.kalavera