Dear all I want to simulate a decane molecule and I used some of the parameters of a paper. The paper studied only C-C-C-C dihedral parameter. As far As I know, the "CT" show the carbon in the aliphatic hydrocarbons in the OPLS-AA force field. I used the following parameters for decane (for all carbons). Please let me know, if there is any mistakes (I am not sure) ? Is it OK to used the parameter from different source (all of them are selected from the OPLS-AA force field) ?
CB CT 1 0.15100 265265.6 ; Added DSM (from CA-CT) CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file CT CT CT 1 112.700 488.273 ; CHARMM 22 parameter file CT CT HC 1 110.700 313.800 ; CHARMM 22 parameter file HC CT HC 1 107.800 276.144 ; CHARMM 22 parameter file CT CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom HC CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon *new* 11/99 The next question is about the "insert-molecules" and "editconf" commands. I used the following commands: gmx_mpi_d insert-molecules -ci DODECANE_pro.gro -nmol 1 -box 3 3 3 -o DODECANE_box.gro gmx_mpi_d editconf -f DODECANE_pro.gro -o DODECANE_box.gro -c -d 1.0 -bt cubic When I used the " editconf " the equilibration step is OK, but the " insert-molecules " command generate a box which the molecule is at the corner of the box and after equilibration step some parts of the molecule are at the opposite site. The results of the equilibration steps for both commands are shown as follows. Please tell me more about this problem! Any help will highly appreciated. thanks *** insert-molecules *** Potential Energy = 2.91421530260847e+01 Maximum force = 8.55101997869504e+00 on atom 35 Norm of force = 6.37158190082328e+00 ***editconf*** Potential Energy = 2.92081220273667e+01 Maximum force = 9.58502180917751e+00 on atom 34 Norm of force = 7.63991317861568e+00 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
