AMBER Archive (2003)

Subject: SPC/E water model

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Sun May 04 2003 - 16:38:06 CDT

Hi amber users,

I have a box with 216 rigid water molecules (using SPC/E model) and I am
equilibrating it at 300K (using amber 7.0, Irix version).
The density of the system is fine, the only thing that puzzles me is the
positive VDW energy. I did check with the rdparm program the distances
between the oxygen atoms in the model (only for O-O the vdw is defined)
and the average is 2.5A. For this distance, using the A (629362.17) and C
(625.27) and a 6-12 potential I get that the value should be negative. So
in principle the sum over all the atoms within the cutoff should be
negative as well. But the value in the output file is positive.
What am I missing or doing wrong?

A second question: According to Berendsen paper (1987 in which the
parameters for SPC/E were developed) the LJ parameters for the O-O
interaction are A=0.37 (kJ/mol)^(1/6)*nm and B = 0.3428 (kJ/mol)^(1/12)*nm
(V_LJ = (B/r)^12-(A/r)^6).
In amber the potential is V_amber = A/r^12-C/r^6 thus
A_amber=B_berendsen^12=2.074e-5(kcal/mol)^(1/12)*Angs and C_amber=
A_berendsen^6=0.0206 (kcal/mol)^(1/6)*Angs
However the rdparm gives values of 629362.17 and 625.27 respectively.
Why are these values different?

Thank you,
Ioana

Here is my input file.

Heating up the system
 &cntrl
  nmropt = 1,
  imin = 0, irest = 0, ntx = 1,
  ntt = 1, temp0 = 300.0, tautp = 0.2,
  tempi = 100.0, ig = 71277, heat = 0.0, vlimit = 15.0,
  ntp = 1, taup = 0.2, pres0 = 1.0, comp = 44.6, npscal = 1,
  ntb = 2, ntc = 2, ntf = 2, iwrap = 1,
  cut = 6.5, scnb = 2.0, scee = 1.2,
  nstlim = 12500, nscm = 0, t = 0.0, dt = 0.002,
  ntwe = 0, ntwx = 500, ntpr = 100, ntwr = 0,
 &end
 &wt
   type='TEMP0', istep1 = 0, istep2 = 500,
                  value1 = 100.0, value2 = 300.0,
 &end
 &wt
   type='TEMP0', istep1 = 500, istep2 = 12500,
                  value1 = 300.0, value2 = 300.0,
 &end
 &wt
  type='END',
 &end
 &rst
  iat = 0,
 &end

Here is the last step from the heating run.

 NSTEP = 12500 TIME(PS) = 25.000 TEMP(K) = 289.10 PRESS = -3.2
 Etot = -2031.5201 EKtot = 372.2684 EPtot = -2403.7884
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 449.5797
 EELEC = -2853.3682 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 178.7273 VIRIAL = 179.1782 VOLUME = 6440.7598
                                                Density = 1.0033
 Ewald error estimate: 0.8572E-03
===============================================================================
                      NMR restraints for step 12500
 Energy (this step): Bond = 0.000 Angle = 0.000 Torsion = 0.000
 Energy (tot. run) : Bond = 0.000 Angle = 0.000 Torsion = 0.000

 DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
            This step Entire run This step Entire run
           ave. rms ave. rms ave. rms ave. rms
 Bond 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================