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

James Starlight jmsstarlight at gmail.com
Mon Apr 16 09:06:32 CEST 2012

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?

2 With applied network of disres applied on backbone atoms of the helix
elements of my protein within Rc=1nm.

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 ).

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