Re: Re: pressure vs density tip3p

From: Roy Kimura (roy.kimura_at_bms.com)
Date: Tue Aug 28 2007 - 07:38:48 CDT

Thank you all for your replies. I think Peter's suggestion is likely the
answer: I am indeed using PME and the reported density is very close to
my observation.

Adam,
 From my experience, fluctuations on the order of ~1000 atm is normal
and, as you say, I think your observed low density is most likely due to
your hydrophobic solute.

Roy

Adam Fraser wrote:

> I too have tried using Nose-Hoover Langevin piston to simulate in NPT
> on a small system (20x20x50) including two hydrocarbons (C16H34). The
> average pressure came close to 1.0 atm (what I was going for), but the
> fluctuations were +/- 1000atm. This scale of fluctuation is normal
> for NPT? I was expecting the pressure readouts to be nearly
> constant. I calculated the density of the system and it turned out to
> be ~0.83 which accounted for a nano bubble that emerged during
> simulation, still I was surprised Solvate 1.3 didn't create a system
> closer to 0.99 density. Do you think this is simply because of the 2
> hydrocarbons?
>
> My apologies for having more questions than answers, my hopes are that
> this response will serendipitously inspire you towards the answer
> you're looking for.
>
> Best,
> -Adam
>
>
>
> On 8/27/07, *Roy Kimura* <roy.kimura_at_bms.com
> <mailto:roy.kimura_at_bms.com>> 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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