[gmx-users] Re: Simulation in the high temperature conditions
jmsstarlight at gmail.com
Mon Apr 16 15:19:26 CEST 2012
I've applied disres on each backbone atom of my potein within cutoff
distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to
decrease overall ammount of the restains in my itp file. Also such value (
1nm) was selected because of the relatively tight packing of the alpha
helices in the TM buddle of membrane protein.
The selected values for disre_dist, disre_up2 and disre_frac were 1, 1.2
and 0.5 nm respectually . Also I've made disres with 1 and 0 nm values but
I have not noticed any difference in the resulted behaviour of the
constrained system. As the consequence I have not clearly realise what
exactly is the disre_frac and in what exactly cases this option could be
This is an example of my output itp file
[ distance_restraints ]
; i j ? label funct lo up1 up2 weight
1 5 1 0 1 0 1.64731 2.64731 1
1 10 1 1 1 0 1.7326 2.7326 1
1 12 1 2 1 0 1.83886 2.83886 1
1 14 1 3 1 0 1.96079 2.96079 1
1 15 1 4 1 0 2.03503 3.03503 1
1 17 1 5 1 0 1.99007 2.99007 1
1 19 1 6 1 0 2.08879 3.08879 1
1 27 1 7 1 0 2.13916 3.13916 1
1 29 1 8 1 0 2.27147 3.27147 1
1 30 1 9 1 0 2.35793 3.35793 1
I've made 10 ns simulation of such system and observe rapid shrinking of my
protein starting with first 100ps like the distances that I chose were too
small and forces shrink my protein. But when I've tried larger distance
value for disre_dist my protein denatured rapidly as no disres were
So the main question is How I could specify this disre values if I want to
restrain the motion of the helixes of my protein within disre value ( e.g
10 A) relatively current confrmation ?
16 апреля 2012 г. 15:05 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:
> 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
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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