From: Dong Luo (us917_at_yahoo.com)
Date: Fri Jul 10 2009 - 08:13:56 CDT
Basically all atom simulation is not suitable for conformational sampling yet especially for folding process IMO. Based on my experience, it's only possible for a peptide less than 30 residues and may only work for alpha helix as expected secondary structure in case of Charmm force field. I'm not sure of martini force field. Alternatively, I started with full folded helix structure and observe it unfolds, it is faster than the folding process. And heat annealing (by controlling the temperature) is employed to accelerate it.
From: doty alexiou <doty_alexiou_at_hotmail.com>
To: namd-list <namd-l_at_ks.uiuc.edu>
Sent: Friday, July 10, 2009 4:00:37 AM
Subject: namd-l: protein folding
Hi.I am running an NAMD simulation of a protein(folding process) using the extended martini foce field.The simulation has run about 70-80 ns(323 k,timestep 10,PBC,in water,RMSD is about 18 till now).Up until now,there is no sign of the expected secondary structure of the protein.Is there any suggestion about what could be wrong or if i should expect it longer?Thank u.
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