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?
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!
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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Received on Tue May 25 2010 - 08:00:13 PDT
