Re: Re: pressure vs density tip3p

From: Vincent Kraeutler (
Date: Mon Aug 27 2007 - 16:55:47 CDT

going to a nanosecond or two certainly wouldn't hurt ;-)

you may want to look at rdf's and possibly water dipole orientation
distributions to make sure you're converging.


Roy Kimura wrote:
> Actually, after typing this I realize the error bars bring my observed
> value very close to the experimental value 0.997, but it still does
> not explain the reported value for TIP3P (1.002) and the systematic
> trend I observed with increasing pressure. Perhaps all I need to do is
> run longer?
> Roy
> Roy Kimura wrote:
>> Dear NAMD group,
>> I have been running boxes of pure water (216 TIP3P, starting box size
>> ~ 18.83 angstrom/side periodic box) in the NPT ensemble using the
>> Nose-Hoover Langevin piston method and temperature coupling (after
>> 100 ps equilibration with velocity rescaling up to 298K). I am
>> running at 1.0 atm pressure and 298 K but when I compute the water
>> density during a 500 ps run by dividing the mass of the simulated
>> water (216 * 18.016 / 6.022e23 grams) with the reported volume, I am
>> getting an average value of about 0.978 +/- 0.018 which is much less
>> than the values reported in the literature for TIP3P water (about
>> 1.002, although experimentally it should be about 0.997). I checked
>> the time plots of all relevant values (temperature, pressure, volume,
>> density) and I am seeing no observable drift, i.e., the system looks
>> to be settled down correctly). The average pressure value (-4.8 atm)
>> was also reasonably close to the target pressure (1.0) given the
>> fluctuations of about +/- 840 atm. After simulating at various
>> pressures (1.0 atm, 50, 100 , 500, 1000, 5000), I found the pressure
>> vs density relation to be linear, and a regression line indicated
>> that in order to obtain 0.997 density, one needs to run at
>> approximately 356 atm. Has anyone else seen this type of behavior? I
>> have been checking the literature values and all papers I have found
>> report the opposite trend (i.e., TIP3P appears to be slightly too
>> dense at 1 atm 298K). I have thought that maybe the box size is too
>> small -- however, a few of the oft-cited original TIP3P papers (1983,
>> 1985) by the Jorgensen group has used the same system size. I would
>> appreciate it if anyone has any insights into this. Thank you very much.
>> Roy

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