[gmx-users] RE: g_rdf

[Junfang.Zhang at csiro.au]

Hi David,

I am simulating the system of water+methane. Can you please let me know
how to use g_rdf to analyze the radial distribution around a specific
set of particles, for example, O-O O-H H-H CH4-O or CH4-CH4.

The topology file is as follows,

;
;  Metahne and water                         
;
#include "ffmet.itp"

[ moleculetype ] 
; Name            nrexcl 
       CH4       2
[ atoms ] 
      1     C4         1  CH4    C4         1     0.0000    12.0100

[ bonds ]

[ pairs ]

[ angles ]

[ dihedrals ]

[ moleculetype ]
; molname	nrexcl
SOL		2

[ atoms ]
; id	at type	res nr 	residu name	at name	cg nr	charge
1	opls_115	1	SOL	MW1	1      -1.04   0.0000
2	opls_114	1	SOL	HW2	1	0.52   1.00800
3	opls_114	1	SOL	HW3	1	0.52   1.00800
4	opls_113	1	SOL	OW4	1	0      15.99940

#ifdef FLEXIBLE
[ bonds ]
; i	j	funct	length	force.c.
4	2	1	0.09572	502416.0 0.09572	502416.0 
4	3	1	0.09572	502416.0 0.09572	502416.0 
	
[ angles ]
; i	j	k	funct	angle	force.c.
2	4	3	1	104.52	628.02	104.52	628.02	

#else
[ constraints ]
; i	funct	doh	dhh
4	2	1	0.09572
4	3	1	0.09572
3	2	1	0.15139

[ exclusions ]
1	2	3	4
2	1	3	4
3	1	2	4
4	1	2	3
#endif



[ dummies3 ]
; Dummy from			funct	a		b
1	4	2	3	1	0.128012065	0.128012065

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ system ]
; Name
Molecular Crystal

[ molecules ]
; Compound        #mols
       CH4        8
       SOL        213

ffmet.itp is as follows,

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
     1       3        yes      0.5     0.5  

[ atomtypes ]
opls_115  1.00000       0.000       A 0.00000E+00 0.00000E+00
opls_114  1.00000       0.000       A 0.00000E+00 0.00000E+00
opls_113  1.00000       0.000       A 3.15365e-01  6.48520e-01
C4        1.00000       0.000       A 3.50000e-01  2.76144e-01

[ nonbond_params ]
 C4   opls_113    1      3.704000E-01   1.1359277e+00



Regards and thanks,

Jane