[gmx-users] protein/membrane simulation parameters

N-J.M. Macaluso njmm2 at cam.ac.uk
Tue Nov 6 17:56:50 CET 2007


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.

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


Max Macaluso  

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