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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