AMBER: SHAKE - ntc = 3

From: Jennie Thomas <jenniet.uci.edu>
Date: Fri, 06 Jan 2006 17:05:09 -0800

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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat Jan 07 2006 - 06:10:05 PST
Custom Search