Re: trouble with MC
Posted: Tue May 05, 2009 2:38 pm
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
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