[gmx-users] Re: Simulation in the high temperature conditions

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 16 13:05:34 CEST 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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