[gmx-users] combination rules -- the part aboutthecombinationrules
shuangxingdai at gmail.com
Wed Feb 25 19:26:52 CET 2009
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.Abraham at 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
> You also shouldn't be using ffgmx for a new simulation, because it has been
> deprecated for years now.
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