[AMBER] heat capacity

From: Ahmet yıldırım <ahmedo047.gmail.com>
Date: Fri, 20 Mar 2015 21:07:34 +0100

Dear users,

I am trying to calculate the heat capacity at constant volume of 1000 water
molecules (tip3p). Firstly I did 10 ns NPT simulation, with
Parinello-Rahman Barostat. And then I performed 100 ps NVT simulation, with
saving time 5 fs. But the pressure of system fluctuates about 100 bar at
NVT simulation. That means the system hasn't reached equilibrium. And the
heat capacity results are not in good agreement with experiment.

-The pressure fluctuations of 100 bar are normal for a normal MD
simulation, right? But it isn't normal for NVT simulation?

-Which the barostat and thermostat do you suggest for NPT simulation? And

-Which the thermostat do you suggest for NVT simulation for liquids? And

-Dear Prof. David A. Case, can you please suggest me some good
"Thermodynamic/Statistical Physics" and "Statistical Physics of Proteins"
books explaining the heat capacity, entropy, partition function and free
energy topics. It will be good if they include both theory and the story of
theory (equation). Especially the story is very important :)

Thanks in advance

Ahmet Yıldırım
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Received on Fri Mar 20 2015 - 13:30:02 PDT
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