From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Fri Mar 15 2013 - 11:25:58 CDT
Dear NAMD users,
I have a question regarding the smd simulation using NAMD. I am pulling off a peptide from a surface (surface is fixed) using smd with force constant of 6 kcal/mol/Ang^2 and pulling velocity of5x10^-6 Ang/fs. My problem is the forces that are printed in the output are unreasonably highe!
e.g. at step 100, the center of mass of peptide has been moved ~0.1 Ang in z-direction. The smd force printed in the output is fz~-43 and I assume the units are kcal/mol/Ang
but this is so high! Doing a rough calculation for force Fz=k(vt-z+z0)= 6(5*10^-6 -0.1) ~-0.6 kcal/mol/Ang
can anyone please help me with this?
I will appreciate it
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