[gmx-users] Buckingham interactions
Mark.Abraham at anu.edu.au
Tue Aug 30 18:54:27 CEST 2011
On 31/08/2011 2:18 AM, xiaojing gong wrote:
> Dear all
> I want to use Buckingham interactions. And I read the manual, but I
> still have some questions for asking:
> 1 ) I need to write the BN Buckingham interactions in the
> format of GMX. see the following:
> Buckingham a(ev) b(nm) C(ev nm^6)
> B-B 6260 0.1 0
> B-N 33 0.7 0
> N-N 4300 0.12 0
> where shall I put the [defaults] lines, could I put these
> in mydefined.itp file?
You can't put these in a molecule .itp file. These lines go in the
forcefield.itp file that is #included at the beginning of normal .top
files. There can only be one [defaults] in your whole .top, including
the #included files.
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 2 1 no 1.0 1.0
> 2) There are three parameters for Buckingham interactions, can
> I write as in the following way?
> [ atomtypes ]
> ;type mass charge ptype a b C6
> B 30.07 1.15 A ?? ?? ??
> N 14.01 -1.15 A ?? ?? ??
Sure. What's the alternative?
> 3) The given Buckingham interaction parameter of B-N may not obey any
> combine rules provided in GMX, what shall I do?
You need to provide suitable [nonbond_params] lines. See manual section
> I will be appreciate it if you can give me some suggestions!
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