[AMBER] SHAKE flucatuation

From: Zhiye Tang <ztang006.ucr.edu>
Date: Thu, 10 Oct 2013 11:54:30 -0700


I ran a MD simulation with pmemd.cuda for a pure water box of 1994 water
molecules with SHAKE algorithm turned on. But when I checked the bond
length and H-O-H angle of the water molecules, they still fluctuated for
around 0.1~0.2. In my case I need to make the water molecule perfectly

The input file of a test run is given below,

 imin=0, irest=1, ntx=5,
 nstlim=1000, dt=0.001,
 ntt=3, temp0=30, ig=-1, tautp=5.0,
 ntp=0, ntb=1,
 ntf=2, ntc=2, tol=0.000001,
 cut=8.0, nsnb=1,
 ntpr=1, ntwr=1, ntwx=1, ntwe=1, ntwv=1,
 nfft1=40, nfft2=40, nfft3=40,

I want to know if SHAKE algorithm restrain the bond length of O-H and H-H
restrictly or it still allows some flucatuation, or if there are some other
parameters I need to turn on to make the bond length perfectly restrict.

Thank you in advance,
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Received on Thu Oct 10 2013 - 12:00:04 PDT
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