Justin, Thank you so much for your help! That was really helpful.
It seems that I simply append my [ nonbond_params ] section to the end of my ffnonbonded.itp file. However, if I ONLY have this: --- ; ffnonbonded.itp [ atomtypes ] ;type at.n mass charge ptype sig eps ; all of the liquid atomtypes ; ... [ nonbond_params ] ; i j func sig eps mywall N 1 0.29750 4.56912 mywall C 1 0.31200 3.07524 mywall H 1 0.26170 1.17675 mywall B 1 0.31225 3.48667 mywall F 1 0.28974 2.82420 --- then I get an error message saying that atomtype mywall does not exist. However, if I simply add a bogus entry for mywall in the [ atomtypes ] section of ffnonbonded.itp, then grompp runs fine: --- ; ffnonbonded.itp [ atomtypes ] ;type at.n mass charge ptype sig eps mywall 6 12.01100 0.000 A 0.00000e-1 0.00000e-1 ; bogus sig and eps ; all of the liquid atomtypes ; ... [ nonbond_params ] ; i j func sig eps mywall N 1 0.29750 4.56912 mywall C 1 0.31200 3.07524 mywall H 1 0.26170 1.17675 mywall B 1 0.31225 3.48667 mywall F 1 0.28974 2.82420 --- Is there any way that I can verify that the code is actually using the parameters for mywall in the [ nonbond_params ] section, rather than the bogus parameters (0 for sig and eps) for mywall in the [ atomtypes ] section? Thank you kindly! Andrew DeYoung Carnegie Mellon University -- 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
