[gmx-users] on NVE and pressure

lorix Loris.Moretti at pharm.unige.ch
Mon Apr 16 09:40:58 CEST 2007

Hi everybody,

I am simulating a protein (approximately 5000 atoms) in water (35000 
atoms). The protein is out of a thermodynamic equilibrium because I 
modified a crystallographic structure of one of its conformation (which 
showed stability with MD). Thus, my aim would be to let the system 
evolve to a new equilibrium. I am expecting a conformation for the 
protein smaller in size than the starting point.
I had several simulations with Temperature and pressure coupling and now 
I have decided to go for NVE (after a prior equilibration with TP 
controls for 300 K and 1 bar) , the decision is mainly because I do not 
want to affect the evolution of atom velocities during the simulation.
With the NVE ensemble after 2 nsec I have an average  value for 
Temperature about 285 K while the Pressure average value is around -230 
bar. The temperature is clearly fine. While the big negative value for 
pressure is meaning that the system wants to contract  if I understood 
correctly ? How does this pressure affect the system? Have I to consider 
the pressure just like a tendency of the system either to contract or to 

thanks for any suggestion

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