VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Thu May 12 2016 - 04:02:24 CDT

Dear VMD users, When I inspect some of my namd trajectories of a protein containing several chains, I find that a certain chain may suddenly seperate from other part of the protein, and this phenomenon seems correspond to the situation in which this chain move out of the water box. The new location of the chain that moves out seems to be symmetry to its original site--it seems to bind to the left part of the protein in another water box although it is invisible. Could you tell me whether I am right or not? If I am right, is there a way to rectify to trajectory?Thanks in advance!