Hello, I am trying to run simulation of graphene oxide. I have 16 carbon atoms of same type. I am using opls force field. could make the .itp file and pasted here
[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_type mass charge ptype sigma epsilon opls_071 CG 6 12.01100 0.00 A 3.50000e-01 2.92880e-01 opls_072 CO 6 12.01100 0.265 A 3.50000e-01 3.59824e-01 opls_116 OH 8 15.99940 -0.683 A 3.12000e-01 7.11280e-01 opls_117 HO 1 1.00800 0.418 A 0.00000 0.00000 [ bondtypes ] ; i j func b0 kb CO OH 1 0.14100 133888.0 OH HO 1 0.09600 231375.0 CG CG 1 0.14000 392459.2 ; TRP,TYR,PHE CG CO 1 0.14000 392459.2 ; TRP,TYR,PHE [ angletypes ] ; i j k func th0 cth CG CO OH 1 90.000 292.880 CO OH HO 1 108.500 230.120 CG CG CG 1 120.000 527.184 ; TYR(OL) [ dihedraltypes ] ; i j k l func coefficients ; OPLS Fourier function (func=5) CJ CJ CJ CJ 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; CG CO OH HO 3 0.00000 0.00000 6.27600 0.00000 CG CG CO OH 3 7.15882 -2.09200 2.77399 0.00000 My question how can I step for the parameters ffoplsaa.rtp file. I made the parameters as follow [ SMA ] [ atoms ] CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CO opls_072 0.265 2 CG opls_071 0.00 1 CG opls_071 0.00 1 CO opls_072 0.265 2 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 OH opls_116 -0.683 3 HO opls_117 0.000 4 OH opls_116 -0.683 3 HO opls_117 0.000 4 [ bonds ] CG CG CG CO CO OH OH HO I am geting trouble to create .top file using pdb2gmx. Can you tell how to set up force field parameter for graphene. I am usinng Gromacs VERSION 4.0.7. Thanks Nilesh -- 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