Re: [AMBER] Problem about Sander with large system

From: Tom Williams <dnaafm.gmail.com>
Date: Tue, 25 May 2010 07:55:09 -0700

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
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