Denaturation via increased temperature

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Aug 15 2011 - 04:11:06 CDT

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

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