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

James Starlight jmsstarlight at gmail.com
Thu Apr 19 08:55:34 CEST 2012


I've tested default disres applied to my protein under high temperature

I've observed that default disre_dist as well as its values up to 0.3 nm in
general prevent destabilisation of my protein under non-native conditions
allowing some dynamics of the restrained regions ( I've not used disre_frac
in all this experiments). But starting from the values of 0.5 nm my protein
was perturbed again.

So the remained questions are

1) Firstly  I'd like to test different cutoff radii for the
increasing\decreasing number of disres but I didnt know how exactly define
this value more accuracy ( previously I've used such cutoff radius for
normal mode analysis of such protein ( in thact case Rc define contacts
between C-alpha atoms ) where the value of 0.8-1 nm gave me good results).

2) My protein consist of some internal water mollecules wich I've defined
explicitly as the separate group (I've coppied coordinates of such waters
from the X-ray structure ).  During dynamics RUN I've noticed that some of
this waters were moved out from receptor to the SOL layer and only several
waters remined in the bounded state with the interoiour of my protein. How
I could specify T_couple and COM groups for such internal waters most
accyracy? I've tried to define it as the part of SOL_Ions layer as well as
in the common group with the protein for both the T_coupling and COM but I
have not noticed any difference between that simulations.

Thanks for help again,


16 апреля 2012 г. 18:09 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

> James Starlight wrote:
>> Justin,
>> Thank you for explanation. Tomorrow I'll try to check results of
>> simulation with the disres applied with its default values as well as with
>> narrower -disre_dist values ( ignorring -disre_frac option at all )  and
>> post here results of such simulations.
>> 1) The cut-off distance wich I've specified was defined with the genrest
>> comand with the -cutoff 1.0 flag. Finally all restrains were apllied on the
>> backbone atoms of alpha helices of the Transmembrane domain of my protein
>> wich I've defined in the index.ndx file. So all loops of my protein were
>> not-restrained at all.
> Ah, I see now.
>  Also I have some small  question about size of output edr file. I've
>> noticed that size of this files of such simulations  (with the disres
>> applied as well as with the -pd flag ) is a very big ( 10-15 gb) Why this
>> occurs and how I could fix it?
> There are energy terms associated with distance restraints.  They cause
> the .edr file to get large very fast if you have a lot of them.  You'll
> have to decrease nstenergy to make the files smaller, or not use the
> restraints.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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