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

[James Starlight]

Justin,


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
helpfull.


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
presented.

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 ?


James

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
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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