Re: Denaturation via increased temperature

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Aug 15 2011 - 06:11:17 CDT

On Monday 15 August 2011 11:38:55 Jernej Zidar wrote:
> Hi Bjoern.
>
Hej Jernej,
thanks for your reply.

> Infolding of proteins typically happens on a much larger time scale. A
> 25-ns simulation is not enough if you want to study protein unfolding
> without using any special techniques (Acelerated Sampling Methods, page
> 148 in the NAMD User's Guide).
>
I am aware of these methods, and the 25ns simulation was just a "dry" run and
serves as starting point for the denaturation run - take it as an "extended
equilibration" run ;-)

> If possible I would first try to extend the trajectory to at least 50 ns.
> Then, if no changes would occur I would use the aforementioned techniques.
>
This was my intend. Currently I have 7ns @50°C if nothing happens at 100ns
I'll first try to boil the protein and if this does not help, I'll try to use
aMD @50°C and see what happens...

Thanks for your suggestions, but this doesn't answer my question about the
correct procedure to set the temperature, or if my approach is sufficient for
my purpose.

Cheers,
Bjoern

> On 15.8.2011, at 17:11, Bjoern Olausson wrote:
> > Hi NAMD users,
> >
> > from lab experiments, I know that my protein starts to unfold at 40°C and
> > is completely unfolded at 50°C
> >
> > I tried to reproduce these results in silico.
> > I ran a simulation for 25ns at 21°C (294.15K)then I restarted the run but
> > with increased temperature. Since I want the protein to unfolded, I did
> > not care about gradually increasing the temperature so I just increased
> > "langevinTemp", "LangevinPistonTemp" and "temperature" to 50°C (323.15K)
> > and commented out "binVelocities" for this run (turning it back on for
> > runs following this one).
> >
> > Checking the output shows, that the temperature and potential energy have
> > increased as expected. Still I am wondering if this is approach is
> > correct, isn't it? Is it more appropriate to use "reassignTemp" and
> > leave the rest as it is? Something like:
> >
> > set temp 294.15
> > [...]
> > binCoordinates $inputname.restart.coor
> > binVelocities $inputname.restart.vel
> > extendedSystem $inputname.restart.xsc
> > [...]
> > langevinTemp $temp
> > LangevinPistonTemp $temp
> > [...]
> > #temperature $temp
> > reassignFreq 100
> > reassignTemp 323.15 294.15
> > reassignIncr 0.3
> > reassignHold 323.15
> > run 500000
> >
> >
> > I guess the temperature will stay at 323.15K when I use "binVelocities"
> > to restart the above run, won't it?
> > Do I have to adjust "langevinTemp" and "LangevinPistonTemp" to match
> > "reassignHold" in the config file for the following runs?
> >
> > Thanks for any hints or other useful comments,
> > Bjoern
> >
> > --
> > Bjoern Olausson
> > Martin-Luther-Universität Halle-Wittenberg
> > Fachbereich Biochemie/Biotechnologie
> > Kurt-Mothes-Str. 3
> > 06120 Halle/Saale
> >
> > Phone: +49-345-55-24942

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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