Re: Problem about the energy change of refold of SMD protein

From: Marcos Sotomayor (
Date: Thu Apr 06 2006 - 00:30:44 CDT


Assuming you are running on the NVE ensemble (TOTAL energy constant, as
done in the tutorial), then the TOTAL energy will change only if an
external (time-independent) force is applied to the system (Work done = force
x distance). Therefore, when you turn the force off, the system will
continue running at the same constant energy (If you switch the force to
half or a smaller value than the original force, then you should be able
to see how the energy decreases).

Note, however, that the tutorial SMD simulations deal with the protein
in vacuum, i.e., without solvent. If you had solvent, then when you turn
the force off, the protein likely will reduce its energy (just the
protein) while the energy of the system (protein + solvent) will still
remain constant.


On Thu, 6 Apr 2006, TCWu wrote:

> 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:
> M.Phone: 090-4046-9249 Fax:+018-884-6098
> Graduate School of Medcine, Akita University
> 010-8543 1-1-1, Hondo, Akita City, Akita, Japan
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