From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon May 23 2016 - 21:01:23 CDT
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> wrote:
> 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,
> 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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