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

[Mark Abraham]

On 19/04/2012 4:55 PM, James Starlight wrote:
> Justin,
>
>
> I've tested default disres applied to my protein under high 
> temperature condiitions.
>
> 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.

Diffusion in and out of receptors is physical - you may not want to 
prevent that. At high temperatures the rate of diffusion will increase, 
and this is yet another problem with your attempted approach.

> How I could specify T_couple and COM groups for such internal waters 
> most accyracy?

COM removal is not for preventing a group of atoms from moving. Maybe a 
COM virtual site with a position restraint would achieve that, but if 
you really need to keep some water in the receptor, you need to put 
position restraints on those waters (and pray that your results mean 
something and people have a reason to believe you).

Mark

> 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,
>
>
> James
>
> 16 ?????? 2012 ?. 18:09 ???????????? Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> ???????:
>
>
>
>     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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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