I am running a protein-water simulation. The system contains 7787 protein
atoms and some 110000 (approx.) water molecules. I first minimised the
system and then heated it to 300 K during 40ps. Then I started the NPT
simulation with a taup value of 0.5. The density value written in the
output file saturates at 0.97 and does not rise further. To check if the
length of the md simulation is an issue, I ran the NPT for 3 ns, but again
got the same result. Isn't it that the value of density that I get must be
nearly equal to 1, which is the density of water. Can you tell me the
possible reason why I am getting a value of 0.97.
A quick help will be gratefully appreciated.
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Received on Thu Aug 22 2013 - 11:30:02 PDT
