Hey,

 

NPT is not the appropriate way to do this kind of simulations. I am not sure 
whether or not the water models available for classic MD simulations are able 
to reproduce the phase behavior. Indeed what you see when your system explodes 
and gets huge is the water evaporating. What is generally done is to allow the 
system to reach the density of liquid water at the temperature that you desire 
(see the Dagget's papers of that) and then use NVT for the rest of the 
simulation. 

Regarding the kinetics of the process it is up to the protein. There are some 
proteins that unfold really fast and others reallly really slow. For instance, 
on one of my systems i have to simulate 50 ns at 600 K to only see a 40% 
decrease in structure. 

As you may already imagine, the pressure gets quite high in these kind of 
simulations. Extreme pressure can also induce protein unfolding, but the 
depence here is again protein dependent since moderately high pressure tends to 
stabilize the structure. Of course what is moderate and what is high is case 
dependent.

Please consider also that biomolecular forcefields were not designed with these 
extreme temperatures in mind, so while doing high temperature induced unfolding 
you are taking the FF to the limit and you should be extremely careful of what 
kind of conclusion you obtain from your simulation.

 

Regards

 

Felipe
----Mensaje original----De: chris.neale@utoronto.caFecha: 16-jun-2011 
12:58Para: <gmx-users@gromacs.org>Asunto: [gmx-users] Can&amp;#39;t unfold the 
proteinDear Hsin-Lin:I am no expert in this area. I am just saying that if you 
get  densities that are way too low in NPT, then you might alleviate this  
problem with NVT.In fact, I would personally do this in vacuum without pbc and 
use the  sd integrator. Then you can sample extended conformations. I'd  
consider this a method to generate unfolded conformations that  probably have 
no relation to the true temperature denatured state. But  let's be honest, 
you're never going to come close to Boltzmann  sampling of an unfolded state in 
300 ns so why bother with the water?Your link ( 
http://manual.gromacs.org/online/protunf.html ) is only  concerned with 
analysis, so it is irrelevant.If you are determined to use NPT then I suppose 
that you could use the  Berendsen barostat (more stable in simulations but you 
get the wrong  ensemble) with a very low compressibility. That's about all I 
can say,  perhaps somebody else will comment.Good luck,Chris.-- original 
message --Dear Chris,Thank you for your reply.My protein is very stable.I 
simulated it in 300ns in 300K before but there was almost no change.That's why 
I want to do denaturation now.I want to start a new simulation on the protein 
which is unfolded.And I'll read the paper you told me.Thank you.But I don't 
understand what you recommend me to do.You use 3000K on your protein and the 
protein unfolded.I use 600K on my protein but the system explode(box become 
very big  and protein locate at corner).I saw the second way on this 
web,http://manual.gromacs.org/online/protunf.htmlBut it also useless to me.And 
in my mdp I use thermostat and barostat, which means my system is NPT.Does 
anything wrong in my methods?Sincerely yours,Hsin-Lin--gmx-users mailing list   
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