[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



[ 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

More information about the gromacs.org_gmx-users mailing list