Thanks Ross.
On Fri, Aug 23, 2013 at 12:05 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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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>
>
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Received on Thu Aug 22 2013 - 12:00:03 PDT
