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
5.3.2
Mark
I will be appreciate it if you can give me some suggestions!
XJ
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