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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php