From: Jernej Zidar (jernej.zidar_at_gmail.com)
Date: Mon Aug 15 2011 - 04:38:55 CDT
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).
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.
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 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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