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.
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
> 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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