[gmx-users] Fw: ionic liquids

Mon May 2 08:36:34 CEST 2011

 

				-- Original Message --

				From: prema.a at iiserpune.ac.in

				To: vvchaban at gmail.com

				Date: Mon, 2 May 2011 11:29:44 +0530 (GMT+05:30)

				Subject: ionic liquids

				
				sir,

				I am grateful regarding your reply. The reported density for [bmim][bf4] system is 1.198 g/cm3.I was wondering whether you asked for the topology that I am using for my calculation or the one that Tsuzuki.et.al.(one I am referring) have used. Well, following is the toopology that I have created for my system.

				
				; File 'bmim.top' was generated

				; By user: onbekend (0)

				; On host: onbekend

				; At date: Fri Apr 15 18:03:14 2011

				;

				; This is a include topology file

				;

				; It was generated using program:

				; Generated by x2top

				;

				; Command line was:

				; g_x2top_d -f boxbmim.pdb -o bmim.top

				;

				; Force field was read from the standard Gromacs share directory.

				;

				
				; Include forcefield parameters

				#include "oplsaa.ff/forcefield.itp"

				
				[ moleculetype ]

				; Name nrexcl

				BIM 3

				
				[ atoms ]

				; nr type resnr residue atom cgnr charge mass typeB chargeB massB

				1 opls_557 1 BIM NA 1 0.24 14.0067 ; qtot 0.24

				2 opls_560 1 BIM CW 2 -0.16 12.011 ; qtot 0.74

				3 opls_561 1 BIM CW 3 -0.27 12.011 ; qtot 1.24

				4 opls_557 1 BIM NA 4 0.32 14.0067 ; qtot 1.48

				5 opls_558 1 BIM CR 5 -0.22 12.011 ; qtot 1.26

				6 opls_905 1 BIM C1 6 -0.35 12.011 ; qtot 0.91

				7 opls_908 1 BIM C1 7 -0.14 12.011 ; qtot 0.77

				8 opls_136 1 BIM C2 8 -0.12 12.011 ; qtot 0.65

				9 opls_136 1 BIM CS 9 -0.12 12.011 ; qtot 0.53

				10 opls_135 1 BIM CT 10 -0.18 12.011 ; qtot 0.35

				11 opls_565 1 BIM HA 2 0.23 1.008 ; qtot 0.41

				12 opls_564 1 BIM HA 3 0.27 1.008 ; qtot 0.47

				13 opls_563 1 BIM HA 5 0.25 1.008 ; qtot 0.53

				14 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.59

				15 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.65

				16 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.71

				17 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.77

				18 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.83

				19 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.89

				20 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.95

				21 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.01

				22 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.07

				23 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.13

				24 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.19

				25 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.25

				
				[ bonds ]

				; ai aj funct c0 c1 c2 c3

				1 2 1 0.1372 178656.8

				1 5 1 0.1340 199576.8

				1 6 1 0.1466 141000.8

				2 3 1 0.1375 217568.0

				2 11 1 0.1080 138490.4

				3 4 1 0.1372 178656.8

				3 12 1 0.1080 138490.4

				4 5 1 0.1340 199576.8

				4 7 1 0.1466 141000.8

				5 13 1 0.1080 138490.4

				6 14 1 0.1090 138490.4

				6 15 1 0.1090 138490.4

				6 16 1 0.1090 138490.4

				7 8 1 0.1516 112131.2

				7 17 1 0.1090 138490.4

				7 18 1 0.1090 138490.4

				8 9 1 0.1529 112131.2

				8 19 1 0.1090 138490.4

				8 20 1 0.1090 138490.4

				9 10 1 0.1529 112131.2

				9 21 1 0.1090 138490.4

				9 22 1 0.1090 138490.4

				10 23 1 0.1090 138490.4

				10 24 1 0.1090 138490.4

				10 25 1 0.1090 138490.4

				
				[ pairs ]

				; ai aj funct c0 c1 c2 c3

				1 7 1

				1 12 1

				2 7 1

				2 13 1

				2 14 1

				2 15 1

				2 16 1

				3 6 1

				3 8 1

				3 13 1

				3 17 1

				3 18 1

				4 6 1

				4 9 1

				4 11 1

				4 19 1

				4 20 1

				5 8 1

				5 11 1

				5 12 1

				5 14 1

				5 15 1

				5 16 1

				5 17 1

				5 18 1

				6 11 1

				6 13 1

				7 10 1

				7 12 1

				7 13 1

				7 21 1

				7 22 1

				8 23 1

				8 24 1

				8 25 1

				9 17 1

				9 18 1

				10 19 1

				10 20 1

				11 12 1

				17 19 1

				17 20 1

				18 19 1

				18 20 1

				19 21 1

				19 22 1

				20 21 1

				20 22 1

				21 23 1

				21 24 1

				21 25 1

				22 23 1

				22 24 1

				22 25 1

				
				[ angles ]

				; ai aj ak funct c0 c1 c2 c3

				2 1 5 1 109.0 292.88

				2 1 6 1 125.6 292.88

				5 1 6 1 125.6 292.88

				1 2 3 1 107.1 292.88

				1 2 11 1 122.0 146.44

				3 2 11 1 130.9 146.44

				2 3 4 1 107.1 292.88

				2 3 12 1 130.9 146.44

				4 3 12 1 122.0 146.44

				3 4 5 1 109.0 292.88

				3 4 7 1 125.6 292.88

				5 4 7 1 125.6 292.88

				1 5 4 1 107.8 292.88

				1 5 13 1 126.1 146.44

				4 5 13 1 126.1 146.44

				1 6 14 1 107.2 156.61

				1 6 15 1 107.2 156.61

				1 6 16 1 107.2 156.61

				14 6 15 1 111.5 138.07

				14 6 16 1 111.5 138.07

				15 6 16 1 111.5 138.07

				4 7 8 1 110.7 418.40

				4 7 17 1 107.2 156.61

				4 7 18 1 107.2 156.61

				8 7 17 1 113.7 156.61

				8 7 18 1 113.7 156.61

				17 7 18 1 111.5 138.07

				7 8 9 1 111.4 418.40

				7 8 19 1 110.7 156.61

				7 8 20 1 110.7 156.61

				9 8 19 1 110.7 156.61

				9 8 20 1 110.7 156.61

				19 8 20 1 107.8 138.07

				8 9 10 1 112.0 418.40

				8 9 21 1 110.7 156.61

				8 9 22 1 110.7 156.61

				10 9 21 1 110.7 156.61

				10 9 22 1 110.7 156.61

				21 9 22 1 107.8 138.07

				9 10 23 1 110.7 156.61

				9 10 24 1 110.7 156.61

				9 10 25 1 110.7 156.61

				23 10 24 1 107.8 138.07

				23 10 25 1 107.8 138.07

				24 10 25 1 107.8 138.07

				[ dihedrals ]

				; ai aj ak al funct c0 c1 c2 c3 c4 c5

				5 1 2 3 1 0.0 -12.5520 2

				2 1 5 4 1 0.0 -19.4598 2

				2 1 6 14 1 0.0 0.51882 3

				1 2 3 4 1 0.0 -44.9780 2

				2 3 4 5 1 0.0 -12.5520 2

				3 4 5 1 1 0.0 -19.4598 2

				3 4 7 8 1 0.0 -0.09205 1

				4 7 8 9 1 0.0 -10.9788 1

				7 8 9 10 1 0.0 4.44341 1

				8 9 10 23 1 0.0 1.53134 3

				#include "topbf4.itp"

				
				[ system ]

				; Name

				BIM

				
				[ molecules ]

				; Compound #mols

				BIM 125

				TFB 125

				
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