James Starlight wrote:
Dear Gromacs Users!
By that moments I've completed 2 sets of simulation in high temperature
1- With applied posres on the backbone atoms ( fc= 200 ).
The result was- that the posres prevented motion of the helixes as the
rigid bodies so I've not noticed any conformation sampling.
Question : Could I observe some conformation sampling on that trajectory
by means of some external tricks ? E.g extracting of the eigenvectors
via PCA?
If you've restrained the position of the atoms, there's no trick that can
magically give you a more desirable result. You've limited the ability of atoms
to move, plain and simple.
2 With applied network of disres applied on backbone atoms of the helix
elements of my protein within Rc=1nm.
What does Rc mean here?
As the result of that simulation I've observed distortion of my protein
wich resulted in some kind of shrinking of the helix elements.
Question : How I could specify that disres more correctly ? If I've
observed some kind of shrinking of my protein does it means that Rc was
chosen incorectly or should I define disres in anothe manner ? ( I'have
not quite understand what exatly is the R_fract and in what situation it
could be useful ).
Without seeing your [distance_restraints] directive, it's impossible to comment
aside from saying that if your structure distorted severely, then yes, you did
something wrong. I also don't know what R_fract is.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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