"Bond rotations in the carbon tails were modeled with Ryckaert-Bellemans dihedrals and the corresponding 1,4 interactions removed" (Lindahl and Edholm, Biophys J., 79, 426-433)
When doing a parameter substitution in this way, exactly what 1,4 interactions should be removed? I am using the pope.itp file from Dr. Tieleman's website and my specific question is why, when the double bond is atom 24 to atom 25, does the [pairs] group contain 22-25 and 24-27, but there are no defined [pairs] for 21-24 or 25-28? The general structure around the double bond looks like this: 21 LP2 22 LP2 23 LP2 24 LH1 || double bond 25 LH1 26 LP2 27 LP2 28 LP2 Below I have extracted any reference to atoms 21 to 28 from pope.itp: [ atoms ] 21 LP2 1 POPE C21 7 0 14.0270 ; qtot: 22 LP2 1 POPE C22 8 0 14.0270 ; qtot: 23 LP2 1 POPE C23 9 0 14.0270 ; qtot: 24 LH1 1 POPE C24 10 0 13.0190 ; qtot: 25 LH1 1 POPE C25 11 0 13.0190 ; qtot: 26 LP2 1 POPE C26 12 0 14.0270 ; qtot: 27 LP2 1 POPE C27 13 0 14.0270 ; qtot: 28 LP2 1 POPE C28 14 0 14.0270 ; qtot: [ bonds ] 21 22 1 0.15300E+00 0.33470E+06 22 23 1 0.15300E+00 0.33470E+06 23 24 1 0.15300E+00 0.33470E+06 24 25 1 0.13900E+00 0.41840E+06 ; double bond 25 26 1 0.15300E+00 0.33470E+06 26 27 1 0.15300E+00 0.33470E+06 27 28 1 0.15300E+00 0.33470E+06 [ pairs ] 22 25 1 ; pair around double bond 24 27 1 ; pair around double bond [ angles ] 21 22 23 1 0.11100E+03 0.46020E+03 22 23 24 1 0.11100E+03 0.46020E+03 23 24 25 1 120.000 502.080 ; cis thingies 24 25 26 1 120.000 502.080 ; cis thingies 25 26 27 1 0.11100E+03 0.46020E+03 26 27 28 1 0.11100E+03 0.46020E+03 [dihedrals] 21 22 23 24 3 22 23 24 25 1 0.000 5.858 3 23 24 25 26 2 0.000 167.360 24 25 26 27 1 0.000 5.858 3 25 26 27 28 3 Thanks for any assistance, Chris Neale. _______________________________________________ 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