[gmx-users] protein/membrane simulation parameters

[Stéphane Téletchéa]

N-J.M. Macaluso a écrit :
> Hi,
> 
> I have two questions that may seem quite simple, but I haven't found 
> clear answers to them. It has to do with the md simulation parameters of 
> a solvated protein/membrane system.
> 
> The first question is about temperature. Some papers simulate at 300 K, 
> others at 298 K, and others at physiological temperature (310 K). I 
> decided that simulating at 310 K gives the most "realistic" picture of 
> the system, as that is biological temp. Why do many studies use 300 K? 
> Is it incorrect to use 310 K for this system? The goal of my work is 
> solely to simulate a GPCR and perform virtual screening on it.

First, as answered by Mark Abraham, look at the literature in order to 
see where and how the parameters were developped. most of the time 
parameters are not that easily transferable and you'll need to benchmark 
yourself with your simulation conditions (it should not be that 
different, but since the software is flexible, there is no 'a priori' 
guarantee).

Second, in using membrane simulations, you need to pay attention to the 
lipid glass transition, since those lipids have often hight temperature 
glass transistion, no question why the DPPC simulations are mostly done 
at 323K (and why in publications where the temperature is below 317K the 
lipids tend to from a glass transition).


> I also decided to simulate the system at physiological salt 
> concentration (.15 M [NaCl]). Will this alter the conformation of my 
> protein significantly?

Well, although my answer may not be the common one, i'm against using a 
"physiological" concentration.
PME needs a neutralisation of the system in order to work so i simply 
add enough ioons to have an neutral one.
The "physiological" concentration is non-sense into such a microscopic, 
unique solute (the protein), system. Never forget the "concentration" is 
an average over billions of molecules, transfering this rapidly to such 
a simplified system seems to me quite a rough approach. Furthermore i've 
not seen many papers mentionning the positive role of such density of 
ions, but more often datas about ions artifacts due to water ordering 
around ions. (there are exceptions, of course for example for 
ion-dependent channels, but since you are interested in GPCR ...).
Last, do not forget that in "physiological" conditions, there is a big 
shift in concentrations from the exterior side to the interior side of 
the cell, for either chloride, sodium or potassium. Since there is no 
way to guarantee the shift would be conserved upon the simulation (an 
ion leaving the bottom of the box, on the intracellular side will enter 
the top of the box, on the extracellular side), this is another good 
reason to not disturb the simulations.

You will probably get more input on this, but at least you have some 
arguments ...

Cheers,
Stéphane

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901