Yes, "add parameters for crystalline zinc oxide, which require Buckingham nonbonded interactions", that is what I am doing. I think I have changed all the necessary parts for the Buckingham potential. Is there any direct way to accomplish my goal? Since in ffgmxnb.itp, all the nonbond_params are LJ if the default type is 1. I only changed the parameters for Zn and O to Buckingham parameters. And you said "add your functions in the right form in your [ molecule ] section" , I cannot find the right place to change. And what force field to choose if not ffgmx? Thank you very much. 2009/2/22 Mark Abraham <mark.abra...@anu.edu.au>
> Shuangxing Dai wrote: > >> No. I only changed 3 lines in ffgmxnb.itp. But there are hundreds of lines >> of error informaion like this: >> ERROR 77 [file ffgmxnb.itp, line 144]: >> Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) >> > > Sure, this is predictable. This force field's files come filled with LJ > functions, and the default pertains to all of them. So you can either have > one form or the other. > > The issue is that if the force field generates the functions for > interactions based on the atom types, you can't mix the two types, since the > result is not defined. Sorry I didn't pick this up the first time, but if > you'd had a descriptive header "I'm trying to add parameters for (?) > crystalline zinc oxide, which require Buckingham nonbonded interactions" > then your strategy problem would have been obvious. > > I'm guessing here, but you may not be constrained by the default type if > you just add your functions in the right form in your [ molecule ] section. > This means you don't need to modify the force field files at all! However > you will need to supply a non-bonded interaction manually for any new atom > type with every atom type in your system. Those also seems likely to be > undefined. > > You also shouldn't be using ffgmx for a new simulation, because it has been > deprecated for years now. > > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Shuangxing Dai
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