[gmx-users] linear molecule

[David]

On Tue, 2003-08-05 at 10:01, Yuguang Mu wrote:
> The point is that , as to my knowledge, the dummy particles have no van
> der Waals interaction. But I want to have these, How can I do ?

yes they can.

see this example (from the gmxtest set)
[ defaults ]
;nonbond-type	combinationrule
1		1

; Division of mass over particles is not correct. Do not use
; for production.
[ atomtypes ]
;type	mass	charge	flavor	c6		c12
CMO	21.0	0.27	A	1.3827e-2	3.01e-5
NOO	20.0	-0.40	A	2.1475e-3	2.7734e-6
COO	0.0	0.13	D	2.5687e-3	3.968e-6

[ moleculetype ]
; name		nrexcl
SOL		1

[ atoms ]
;nr	type	resnr	residu	atom	cgnr	charge
1	CMO	1	SOL	Me1	1	0.27
2	NOO	1	SOL	N2	1	-0.40
3	COO	1	SOL	C3	1	0.13


[ constraints ]
;ai	aj	funct	dist
;1	2	1	0.146	1e6
;3	2	1	0.117	1e6
1	2	1	0.263	1e6

[ dummies2 ]
;
;calculating the position of the dummy atom
;
;  X1-----X3---X2
;
;  X3 = A1*X1 + A2*X2
;
;  A1 = 1 - dist(X1-X3)/dist(X1-X2) = 1 - 0.146/0.263 = 0.445
;  A2 = 1 - dist(X3-X2)/dist(X1-X2) = 1 - 0.117/0.263 = 0.555
; Dummy	from		funct	a	b
3	1	2       1	0.445	0.555

[ exclusions ]
1	2	3
2	1	3
3	1	2





-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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