;;;;;; GENERAL SOLVENT TOPOLOGIES
; Last updated 04-12-2012 by DdJ

;;;;;;;;;;;;
;;;;;;;;;;;; ALKANES
;;;;;;;;;;;;

;;;;;; BUTANE
;
; same particle type represents ISOPROPANE

[moleculetype]
; molname 	nrexcl
  BUT 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	C1 	1 	BUT 	C1 	1 	0 

;;;;;; PROPANE 

[moleculetype]
; molname 	nrexcl
  POP 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	C2 	1 	POP 	C 	1 	0 

;;;;;; OCTANE

[moleculetype]
; molname 	nrexcl
  OCT 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	C1 	1 	OCT 	C 	1 	0 
  2 	C1 	1 	OCT 	C 	2 	0 

[bonds]
; i j 	funct 	length 	force.c.
  1 2 	1 	0.47 	1250

;;;;;; DODECANE
;
; same topology represents DECANE

[moleculetype]
; molname 	nrexcl
  DEC 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
 1 	C1 	1 	DEC 	C 	1 	0 
 2 	C1 	1 	DEC 	C 	2 	0 
 3 	C1 	1 	DEC 	C 	3 	0 

[bonds]
; i j 	funct 	length 	force.c.
  1 2 	1 	0.47 	1250
  2 3 	1 	0.47 	1250

[angles]
; i j k 	funct 	angle 	force.c.
  1 2 3 	2 	180.0  	25.0 

;;;;;; HEXADECANE

[moleculetype]
; molname 	nrexcl
  HD 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	C1 	1 	HD 	C 	1 	0 
  2 	C1 	1 	HD 	C 	2 	0 
  3 	C1 	1 	HD 	C 	3 	0 
  4 	C1 	1 	HD 	C 	4 	0 

[bonds]
; i j 	funct 	length 	force.c.
  1 2 	1 	0.47 	1250
  2 3 	1 	0.47 	1250
  3 4 	1 	0.47 	1250

[angles]
; i j k 	funct 	angle 	force.c.
  1 2 3 	2 	180.0 	25.0 
  2 3 4 	2 	180.0 	25.0 

;;;;;; OCTADECANE

[moleculetype]
; molname 	nrexcl
  OD 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	C1 	1 	OD 	C 	1 	0 
  2 	C1 	1 	OD 	C 	2 	0 
  3 	C1 	1 	OD 	C 	3 	0 
  4 	C1 	1 	OD 	C 	4 	0 
  5 	C1 	1 	OD 	C 	5 	0 

[bonds]
; i j 	funct 	length 	force.c.
  1 2 	1 	0.47 	1250
  2 3 	1 	0.47 	1250
  3 4 	1 	0.47 	1250
  4 5 	1 	0.47 	1250

[angles]
; i j k 	funct 	angle 	force.c.
  1 2 3 	2 	180.0 	25.0 
  2 3 4 	2 	180.0 	25.0 
  3 4 5 	2 	180.0 	25.0 

;;;;;; cis-OCTADECENE (with a cis double bond around position w=9)

[moleculetype]
; molname 	nrexcl
  ODE 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1  	C1 	1 	ODE 	C 	1 	0 
  2  	C1 	1 	ODE 	C 	2 	0 
  3  	C3 	1 	ODE 	D  	3 	0 
  4 	C1 	1 	ODE 	C 	4 	0 
  5 	C1 	1 	ODE 	C 	5 	0 

[bonds]
; i j 	funct 	length 	force.c.
  1 2 	1 	0.47 	1250
  2 3 	1 	0.47 	1250
  3 4 	1 	0.47 	1250
  4 5 	1 	0.47 	1250

[angles]
; i j k 	funct 	angle 	force.c.
  1 2 3 	2 	180.0 	25.0 
  2 3 4 	2 	120.0   45.0 
  3 4 5 	2 	180.0 	25.0 

;;;;;; trans-OCTADECENE (with a trans double bond around position w=6)

[moleculetype]
; molname 	nrexcl
  ODT 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1  	C1 	1 	ODT 	C 	1 	0 
  2  	C3 	1 	ODT 	D 	2 	0 
  3  	C1 	1 	ODT 	C  	3 	0 
  4 	C1 	1 	ODT 	C 	4 	0 
  5 	C1 	1 	ODT 	C 	5 	0 

[bonds]
; i j 	funct 	length 	force.c.
  1 2 	1 	0.47 	1250
  2 3 	1 	0.47 	1250
  3 4 	1 	0.47 	1250
  4 5 	1 	0.47 	1250

[angles]
; i j k 	funct 	angle 	force.c.
  1 2 3 	2 	180.0 	45.0 
  2 3 4 	2 	180.0   25.0 
  3 4 5 	2 	180.0 	25.0 


;;;;;; BENZENE
; The benzene topology has been adopted following:
; D.H. de Jong, G. Singh, W.F.D. Bennet, C. Arnarez, T.A. Wassenaar, L.V. Schafer,
; X. Periole, D.P. Tieleman, S.J. Marrink.
; Improved Parameters for the Martini Coarse-Grained Protein Force Field
; J. Chem. Theory Comput., DOI: 10.1021/ct300646g
;
; The bead type changed from SC4 to SC5. This improves the butane-water partitioning
; but does not affect the properties of pure benzene.

[moleculetype]
; molname       nrexcl
  BENZ 		1

[atoms]
; id    type    resnr   residu  atom    cgnr    charge
  1 	SC5 	1 	BENZ 	R1 	1 	0 
  2 	SC5 	1 	BENZ 	R2 	2 	0 
  3 	SC5 	1 	BENZ 	R3 	3 	0 

[constraints]
; i j   funct   length
  1 2 	1 	0.27
  2 3 	1 	0.27
  1 3 	1 	0.27


;;;;;;  CYCLOHEXANE

[moleculetype]
; molname       nrexcl
  CHEX 		1

[atoms]
; id    type    resnr   residu  atom    cgnr    charge
  1 	SC1 	1         CHEX 	R1 	1 	0 
  2 	SC1 	1         CHEX 	R2 	2 	0 
  3 	SC1 	1         CHEX 	R3 	3 	0 

[bonds]
; i j   funct   length  force.c.
  1 2 	1 	0.3 	5000
  2 3 	1 	0.3 	5000
  1 3 	1 	0.3 	5000


;;;;;;;;;;;;
;;;;;;;;;;;; ALCOHOLS
;;;;;;;;;;;;

;;;;;; BUTANOL 

[moleculetype]
; molname 	nrexcl
  BOL 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	Nda 	1 	BOL 	COH 	1 	0 

;;;;;; PROPANOL

[moleculetype]
; molname 	nrexcl
  POL 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	P1 	1 	POL 	COH 	1 	0 

;;;;;; ETHANOL

[moleculetype]
; molname 	nrexcl
  EOL 		1
                                                                                                     
[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	P2 	1 	EOL 	COH 	1 	0
                                                                                                     
;;;;;; OCTANOL

[moleculetype]
; molname 	nrexcl
  OCO 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	P1 	1 	OCO 	PC 	1 	0 
  2 	C1 	1 	OCO 	C 	2 	0 

[bonds]
; i j 	funct 	length 	force.c.
  1 2 	1 	0.47 	1250

;;;;;;;;;;;;
;;;;;;;;;;;; OTHER ORGANIC SOLVENTS 
;;;;;;;;;;;;

;;;;;; CHLOROPROPANE 

[moleculetype]
; molname 	nrexcl
  PRX 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	C3 	1 	PRX 	CX 	1 	0 

;;;;;; CHLOROFORM 

[moleculetype]
; molname 	nrexcl
  CLF 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	C4 	1 	CLF 	CX 	1 	0 

;;;;;; METHYLETHYLSULFIDE 

[moleculetype]
; molname 	nrexcl
  MES 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	C5 	1 	MES 	CS 	1 	0 

;;;;;; ETHER 

[moleculetype]
; molname 	nrexcl
  ETH 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	N0 	1 	ETH 	CO 	1 	0 

;;;;;; PROPANON (ACETON)

[moleculetype]
; molname 	nrexcl
  PON 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	Na 	1 	PON 	CO 	1 	0 

;;;;;; PROPYLAMINE 

[moleculetype]
; molname 	nrexcl
  PAM 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	Nd 	1 	PAM 	CN 	1 	0 

;;;;;; ACETIC ACID

[moleculetype]
; molname 	nrexcl
  ACH 		1 

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	P3 	1 	ACH 	OOH 	1 	0

;;;;;; ACETAMIDE 

[moleculetype]
; molname 	nrexcl
  ACE 		1

[atoms]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge
  1 	P5 	1 	ACE 	NCO 	1 	0 

;;;;;; GLYCERINE TRIOLEATE
;
; provided by Timu Vuorela
; 
; please cite: 
; T. Vuorela, A. Catte, P.S. Niemela, A. Hall, M.T. Hyvonen, S.J. Marrink, M. Karttunen, I. Vattulainen
; Role of lipids in spheroidal high density lipoproteins
; In preparation, 2010.
;

[ moleculetype ]
; molname       nrexcl
TO               1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   C1   1     TO     GLY    1      0
 2   Na   1     TO     ES1    2      0
 3   Na   1     TO     ES2    3      0
 4   Na   1     TO     ES3    4      0
 5   C1   1     TO     C1A    5      0
 6   C3   1     TO     D2A    6      0
 7   C1   1     TO     C3A    7      0
 8   C1   1     TO     C4A    8      0
 9   C1   1     TO     C1B    9      0
 10  C3   1     TO     D2B    10     0
 11  C1   1     TO     C3B    11     0
 12  C1   1     TO     C4B    12     0
 13  C1   1     TO     C1C    13     0
 14  C3   1     TO     D2C    14     0
 15  C1   1     TO     C3C    15     0
 16  C1   1     TO     C4C    16     0

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.47     1250
   1     3    1       0.47     1250
   1     4    1       0.47     1250
   2     5    1       0.47     1250
   5     6    1       0.47     1250
   6     7    1       0.47     1250
   7     8    1       0.47     1250
   3     9    1       0.47     1250
   9     10   1       0.47     1250
   10    11   1       0.47     1250
   11    12   1       0.47     1250
   4     13   1       0.47     1250
   13    14   1       0.47     1250
   14    15   1       0.47     1250
   15    16   1       0.47     1250

[angles]
;  i     j    k     funct   angle  force.c.
   2     1    4       2    60.000  25.0
   2     1    3       2   130.000  25.0
   3     1    4       2   130.000  25.0
   1     2    5       2   180.000  25.0
   2     5    6       2   180.000  25.0
   5     6    7       2   120.000  45.0
   6     7    8       2   180.000  25.0
   1     3    9       2   180.000  25.0
   3     9   10       2   180.000  25.0
   9    10   11       2   120.000  45.0
  10    11   12       2   180.000  25.0
   1     4   13       2   180.000  25.0
   4    13   14       2   180.000  25.0
  13    14   15       2   120.000  45.0
  14    15   16       2   180.000  25.0

