[gmx-users] CHARMM force field : TIP3 LJ parameters
Nicolas SAPAY
nsapay at ucalgary.ca
Fri Sep 15 00:31:20 CEST 2006
Hello everybody,
sorry to bother you with my problems another time. I have checked the
non-bonded parameters from Yuguang Mu's ffcharmmnb.itp. The parameters for
TIP3 atoms (CHARMM's water model) are :
c6 c12
HT 1.008 0.000 A 3.1539699357e-09 1.2921281844e-17
OT 15.999 0.000 A 2.4895403920e-03 2.4347673691e-06
I obtain exactly the same thing according to the combination rule #1 and
my own version of the charmm ff.
The differences happen when the pair HT..OT is combined in
[nonbond-params] (using comb-rule #1 and function #1). Yuguang's
parameters are :
c6 c12
HT OT 1 4.3824474706e-05 1.3719498873e-09
while I obtain :
c6 c12
OT HT 1 2.802131e-06 5.608950e-12
according to chapter 5.6.1, the computation should be C_ij^(M) =
sqrt(C_i^(M) . C_j^(M)) with M = [0,6]. So, for the OT..HT pair :
C_ij(6) = sqrt( 2.490e-03 x 3.154e-09 ) = sqrt( 7.852e-12 ) = 2.802e-06
C_ij(12)= sqrt( 2.435e-06 x 1.292e-17 ) = sqrt( 3.146e-23 ) = 5.609e-12
Has Someone an idea about this difference? Have I missed something? I have
checked several other pairs (with or without CHARMM's 1-4 parameters) :
the problem seem to be limited to the OT..HT pair
cheers
Nicolas
--
[ Nicolas Sapay Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University Dr. NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311
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