I have successfully construct the polymer chain of length 1 using the OPLS force field. The rtp file as follow:
; F2311 - this is an internal residue [ Fre ] [ atoms ] C1 opls_135 -0.568 1 H11 opls_140 0.274 1 H12 opls_140 0.273 1 C2 opls_962 0.373 2 F21 opls_965 -0.165 2 F22 opls_965 -0.159 2 C3 opls_962 0.182 3 F31 opls_965 -0.133 3 F32 opls_965 -0.144 3 C4 opls_963 0.142 4 F4 opls_965 -0.142 4 Cl4 opls_151 0.066 4 [ bonds ] C1 -C4 C1 H11 C1 H12 C1 C2 C2 F21 C2 F22 C2 +C3 C3 F31 C3 F32 C3 C4 C4 F4 C4 Cl4 C4 +C1 ; Terminal f2311 residue ("beginning" of chain) ; designation arbitrary, C1 is -CH3 [ Fbg ] [ atoms ] C1 opls_135 -0.565 1 H11 opls_140 0.198 1 H12 opls_140 0.208 1 H13 opls_140 0.209 1 [ bonds ] C1 H11 C1 H12 C1 H13 ; Terminal f2311 residue ("end" of chain) ; designation arbitrary, C1 is -CH3 [ Fen ] [ atoms ] C1 opls_135 -0.705 1 H11 opls_140 0.248 1 H12 opls_140 0.246 1 H13 opls_140 0.245 1 [ bonds ] C1 H11 C1 H12 C1 H13 -- View this message in context: http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-tp5006328p5006428.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists