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
===============================================================================
Received on Sun May 04 2003 - 22:53:01 PDT
