[gmx-users] protein/membrane simulation parameters

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 7 01:37:44 CET 2007

N-J.M. Macaluso wrote:
> 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? 

Because the authors didn't think about it, or recycled an old parameter 
file, or don't think the temperature will matter given the other 
approximations that are going on, or that their system is often not at 
"core" body temperature and will thus "work" at lower temperatures. 
Another key reason is that their force field was probably parameterized 
using data from a particular temperature, like 298K. Moving to a 
different temperature gives unpredictable results.

> 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.

Likely enough, you will have to make a compromise somewhere.

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

It might. This isn't a question that can be answered in the general case 
:-) You'll want to work out how many ions that will give you for the 
size of your water region.


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