[gmx-users] Loop displacement calculation?
Mark.Abraham at anu.edu.au
Tue Apr 22 07:50:24 CEST 2008
SeungPyo Hong wrote:
> Dear gmx-users,
> (This is not related to my previous question about the failure of the
> simulation. Now I guess that there are some technical problems in our
> cluster system.)
> Hello gmx-users, I am not a quite new user, but still don't know many
> many thing.
> Planning an experiment I hope to listen to your advices.
> Recently I plan to perform free energy calculation to test the stability
> of a loop in a protein.
> To do so, I will select two atoms; one in the backbone atom of the loop
> and the other in the backbone of the protein nearby the loop region.
> Then, those sites are connected by a [ bond ] and the spring constant
> will be changed from 0 to 100 as lambda changes from 0 to 1. (The
> equilibrium length is fixed to 20 A.)
> I am wandering whether this simulation will be generally accepted or not.
How does such a calculation reveal the "stability of [the] loop"? You
need a more precise goal in order to design a calculation to measure
something. Perhaps some more background reading is in order :-)
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