Hello,
On Tue, May 25, 2010 at 10:55 AM, Tom Williams <dnaafm.gmail.com> wrote:
> Dear Prof. Ross
>
> I am confused about your comments: "The solution is constant-pressure
> equilibration."
> You mean the Xleap superimpose/subtract algorithm or my MD run?
>
He means that the way of getting rid of the 'bubbles' (or prevent them in
the first place) is to run NPT.
>
> This is my MD *.in file:
>
> 0-300K constant temp MD
> &cntrl
> imin=0,
> ntb=1,cut=18.0,
> ntc=2, ntf=2,
> tempi=0.0, temp0=300.0,
> ntt=1,iwrap=1,
> nstlim=10000, dt=0.002,
> ntpr=500, ntwx=1000
> /
>
> I had a minimization before the above MD run. Now i used ntr. The result is
> same as ibelly.
> -------------------------------------
> Initial minimisation of our structure
> &cntrl
> imin=1, maxcyc=500, ncyc=300,
> cut=9, ntr=1, ntb=1,
> ntc=2, ntf=2
> /
> Hold protein fixed
> 500.0
> RES 1 129
> END
> END
> -----------------------
> Both of MD and minization are with *NVT* and *not NPT*,right? Why the run
> in NVT still have such difference in water density to result in water
> holes?
> Thanks a lot for your help!
>
Correct. The above simulations (ntb=1) is constant volume. The issue with
NVT is that the size of the periodic box is not permitted to change
(obviously). If there are not enough water molecules in the box to maintain
the proper density, then you may see bubbles start to form. NPT will adjust
the volume of the periodic box to maintain a constant pressure (although,
due to considerations discussed in some detail here on the list, the density
is a better measure of NPT convergence since the pressure fluctuates a
lot). Thus, NPT will reduce the size of the periodic box to maintain
constant pressure/density, thereby getting rid of the bubbles.
Hope this helps,
Jason
>
> Tom
>
>
> On 5/25/10, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> > > Do you think it is because of *ibelly*?
> >
> > No.
> >
> > > Is it because Xleap is not be able to assign water
> > > molecules with correct density and cause this water hole?
> >
> > Yes, it's a consequence of the superimpose/subtract algorithm.
> > The solution is constant-pressure equilibration.
> >
> > Bill
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue May 25 2010 - 08:30:03 PDT
