I am running a simulation of NO3- in water using the following frcmod file:
This is the additional/replacement parameter set for nitrate ion NO3-
MASS
ON 16.000 1.000
NO 14.000 0.000
BOND
ON-ON 500. 2.197
ON-NO 500. 1.269
ANGLE
ON-NO-ON 100. 120.0
ON-ON-ON 0. 60.
NO-ON-ON 0. 30.
DIHE
ON-ON-ON-ON 2 0.0 0.0 2.
ON-ON-ON-NO 2 0.0 0.0 2.
ON-ON-NO-ON 2 0.0 0.0 2.
ON-NO-ON-ON 2 0.0 0.0 2.
NONB
NO 1.88 0.1700
ON 1.80 0.160
In my input file, I have specified ntc=3, so all of the bond lengths
should be fixed. However the O-O bond length (averaged over time) is
about 0.1 Angstroms shorter than the length specified in the force
field Here is the input file for the simulation:
# 100 ps const. vol. / const. temp. production; shake; polarizability
&cntrl
imin = 0,
ntx = 5, irest = 1,
ntpr = 100, ntwr = 100, ntwx = 500,
ntwd = 500,
iwrap = 1,
ntf = 2, ntb = 1,
cut = 12, ipol = 1,
max_field = 8.0, switch_fac = 0.9,
nstlim = 100000, dt = 0.001, t = 0,
ntt = 1, temp0 = 300.0, tautp = 1.0,
ntc = 3, tol = 0.00000000001,
jfastw = 0, watnam = 'PL3',
owtnm = 'O', hwtnm1 = 'H1', hwtnm2 = 'H2',
&end
&ewald
use_pme=1, eedmeth=1, vdwmeth=0
a=30., b=30., c=100.
indmeth=1, diptol=0.0001
&end
Is there any reason why the O-O bond length is not being frozen to the
correct value using SHAKE?
Thanks!
Jennie Thomas
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Received on Sat Jan 07 2006 - 06:10:05 PST
