From: TCWu (tcwu_at_mis.med.akita-u.ac.jp)
Date: Wed Apr 05 2006 - 18:53:35 CDT
Dear NAMD user
I am new user of NAMD and I have done the tutorial all
already. The problem is when I done the SMD of constant force on ubiquitin
then (10 ps), I try to simulated refolding of stretched ubiquitin as same as
Gao M. et. al., done (Biophysical Journal 81(4)2268-2277, 1999). The force
is set to 0 at B column of constant force file and run 50 ps. The extension
seems decrease from 10A to 1 A, but the energy whatever total energy or
kinetic energy, temperature as well, have no any change i.e. the value still
as same as the end of SMD. If the conformation change of ubiquitin reverse
to the original conformation position, the energy should also decrease to
the value nearly as same as the value before SMD, is this correct? Please
help me! Thank you very much!
Sincerely yours
---------------------------------------------
Tsann-Chung Wu
Email: tcwu_at_mis.med.akita-u.ac.jp$B!!(B(Academic)
M.Phone: 090-4046-9249 Fax:+018-884-6098
Graduate School of Medcine, Akita University
$B")(B010-8543$B!!(B 1-1-1, Hondo, Akita City, Akita, Japan
---------------------------------------------
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