AMBER Archive (2003)

Subject: AMBER: NaCl ion pairs in TIP3P water box

From: Nathan A. Baker (baker_at_cholla.wustl.edu)
Date: Wed Sep 24 2003 - 15:13:11 CDT

Hi All --

I feel a bit embarassed asking this question, but I'm completely
stumped. I'm trying to perform MD on a (47 A)^3 box of TIP3P water
with 62 Na+ and 62 Cl- ions (~1 M conc.). Here's my protocol:

1. Set up box of water (TIP3P)
2. Randomly replace water molecules with ions such that no ion is less
   than 6.0 A from any other; generate inpcrd and prmtop (AMBER99)
3. Restrain ions and minimize solvent:

   Minimization of system
   &cntrl
     imin = 1, maxcyc = 5000,
     ncyc = 5000, dx0 = 0.0005, dxm = 0.05,
     ntf = 1, ntb = 1, ntc = 1,
     dielc = 1, cut = 12.0, nsnb = 999,
     ntr = 1,
     lastist = 10000000, lastrst = 10000000,
   &end
   Group input for restrained atoms
   1000.0
   RES 1 124
   END
   END

4. Restrain ions and do 10 ps 50 K dynamics on solvent:

   Equilibration of solvent at 50 K for 10 ps
   &cntrl
     imin = 0, ntx = 1, irest = 0,
     ntwe = 50, ntrx = 1,
     ntf = 2, ntb = 1, ntc = 2,
     cut = 10.0, nsnb = 20, nscm = 500,
     nstlim = 5000, dt = 0.002,
     tempi = 50.0, temp0 = 50.0,
     ntt = 1, ntr = 1,
     lastist = 10000000, lastrst = 10000000,
   &end
   Group input for restrained atoms
   1000.0
   RES 1 124
   END
   END

5. Perform MD at 50, 100, 150, 200, 250, 300 K on whole system:

   Equilibration of the whole system at #TEMP# K for 10 ps
   &cntrl
     imin = 0, ntx = 1, irest = 0,
     ntwe = 50, ntrx = 1,
     ntf = 2, ntb = 1, ntc = 2,
     cut = 10.0, nsnb = 20, nscm = 500,
     nstlim = 5000, dt = 0.002,
     tempi = #TEMP#, temp0 = #TEMP#,
     ntt = 1,
     lastist = 10000000, lastrst = 10000000,
   &end

However, I invariably end up with ion pairs by the time I reach the
150-200 K stage of this procedure. The appearance of ion pairs does
occurs with or without Step 4; I added that as an additional attempt
to keep the ions apart.

Does anyone have an idea what I might be doing wrong here?

Thanks,

Nathan 

-- 
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone:  (314) 362-2040, Fax:  (314) 362-0234
URL:  http://www.biochem.wustl.edu/~baker
PGP key:  http://cholla.wustl.edu/~baker/pubkey.asc

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