From: Faramarz Joodaki (fjoodaki_at_my.uri.edu)
Date: Mon May 23 2016 - 22:44:21 CDT
Thank you very much for your guidance!
The RMS (or stdev) is 1402.12.
The extension from average (7.65) is +/-2000.
The size of my box (in A) is:
cellBasisVector1 24.818 0.000 0.000
cellBasisVector2 0.000 24.872 0.000
cellBasisVector3 0.000 0.000 28.207
cellOrigin 0.000 0.000 0.000
So the volume of the box is 17.41 nm^3.
I checked the temperature and total energy of the system which are constant
over MD simulation. It seems that I am in the equilibrium.
Do I need to make my box smaller? Actually I have one TRP molecule and
water molecules in my box.
It seems that I need to be sure more about the equilibrium.
Another point: My desire pressure is 1atm but I reached to average of 7.65.
On Mon, May 23, 2016 at 10:01 PM, Peter Freddolino <petefred_at_umich.edu>
> The observed fluctuations are also dependent on the water model, which may
> be different in the assumptions made by gromacs. See
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node37.html for a discussion
> and formula. For TIP3P water, with an isothermal compressibility of 6*10^-5
> atm^-1 at 25 C (Jorgensen and Jensen, JCC 1997), and assuming you have
> roughly the right density (which gives a box with a volume of 15.2 nm^3),
> you should get an *RMS* fluctuation of ~200 bar if the theory holds
> perfectly, but practicalities in the approximations needed to run MD are
> why, as noted there, "Much larger fluctuations are regularly observed in
> practice”. So, before going any further — are you sure that your system has
> equilibrated and you’re only considering points after equilibration in your
> analysis? And, is the +/- 2000 atm the maximum extent or the RMS? You
> should be calculating the latter to match up with expectations.
> > On May 23, 2016, at 7:29 PM, Faramarz Joodaki <fjoodaki_at_my.uri.edu>
> > Hi Jeff,
> > Thank you for your response!
> > I read that link. I agree fluctuation for pressure is necessary. But I
> think there is a big fluctuation in my system:
> > My system has 509 water molecules. The pressure of my system is
> fluctuating between -2000 and +2000. The number of steps are 1M and I set
> to report pressure each 100 steps. The average of pressure during this MD
> simulation is 7.65atm.
> > According to the link which you sent me, the fluctuation should be less
> than 500. Because the number of water molecules is 509.
> > I would be so grateful if you could give me some suggestions to decrease
> this amount of fluctuation.
> > Best regards,
> > Faramarz
> > On Mon, May 23, 2016 at 5:06 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> > See: http://www.gromacs.org/Documentation/Terminology/Pressure
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