[gmx-users] Pressure change after NPT equilibriation
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 16 15:24:47 CET 2011
shilpa yadahalli wrote:
> Dear Justin,
> sorry to trouble you again. I want to ask one more thing.
> I saw some of the documentation regarding, and i found that (on d page u
> mentioned frm gromacs), for a box of 216 waters, fluctuations of 500-600
> bar are standard. And for a system of 21600 water molecules ~
> fluctuations of 50-60 bar.
> My system has ~ 5000 to 6000 water molecules. So i should expect
> pressure fluctuations less than 500-600 bar (?).
> If i go acc. to above calculations then i should expect, 600 bar /
> (28)^1/2 = ~ 113.38 bar. [6000/216 water molecules ~ 27.78 ].
> (my run time for npt equlibriation is 600 ps.)
Per the page quoted before, pressure decreases as the root of the number of
particles, not the square of the number of the ratio of molecules :)
You should note that, if I recall, the quoted statistics are for the Berendsen
barostat (a weak coupling algorithm with exponential decay) for a box of pure
water. The Parrinello-Rahman barostat will have larger fluctuations.
> Can you pls explain me regarding.
> Thanks alot,
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* shilpa yadahalli <shilpa_09honey at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wednesday, November 16, 2011 12:02 AM
> *Subject:* Re: [gmx-users] Pressure change after NPT equilibriation
> shilpa yadahalli wrote:
> > After doing NPT simulation I plot pressure and density. How much
> pressure change is considered as normal? I'm getting pressure change +/-
> 500 bar, after doing NPT equilibration for most of my proteins. And for
> one of the protein it is as high as +/- 1000 bar.
> > Can anybody tell me what is the Normal/expected pressure change. My
> temperature is constant 300 K. (I m running simulations at normal
> conditions of temperature and pressure. 300K, 1 bar, using _AMBER99SB_
> FF, protein is globular with 92 amino acids). Log file etc, does not
> shows any warnings and simulation also does not show any inconsistent
> topology shifts.
> > After my production run also, i do not get any warnings. and my rmsd
> is below 0.2.
> > but i am not much happy with the pressure changing so much.
> Sounds completely normal.
> You haven't shown your .mdp settings so it's hard to gauge what you
> should expect, but again, this is expected behavior for the reasons
> described at the above link.
> -- ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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