Distance Analysis for Constant Force Pulling for kinesin neck linker

From: Patriche Simona (s_patriche_at_yahoo.com)
Date: Fri Mar 05 2010 - 05:44:37 CST

Dear NAMD users,
Hi, I am a beginner user of NAMD and I need to some suggestions  about distance  analysis for constant force pulling in case of kinesin neck linker, PDB ID: 1MKJ. First I cut neck linker (which contains 13 amino acids) from this kinesin, I made the psf file and Minimization and Equlibration and Steered Molecular Dynamics. I was very supprised that when I tried to make the graph, distance versus time, for this analysis because  I observed that the distance decreased. The value used  for constant force is 1pN = 0.014425 kcal/mol/A.Thanks ,
Simona Patriche

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