Hi Sourav,
Note that your system is NOT pure water - it is in fact a VERY high
concentration solution of protein - thus it is perfectly reasonable to
expect that the density would not be that of water. Whether the resulting
density should be more or less that of pure water is very dependent on the
nature of your protein. I'm not entirely sure if there are specific rules
for this - related to hydrophobicity for example, or whether predominantly
alpha helix proteins are more dense than beta sheet proteins or vice
versa. Others on the list may be able to comment more.
I'd also note that the density for pure water of 1.0 g/cm^3 is for water
at it's triple point of 277K. As you raise the temperature above this so
the density decreases.
All the best
Ross
On 8/22/13 10:59 AM, "Sourav Purohit" <sour000.gmail.com> wrote:
>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 - 12:00:02 PDT
