On 13/01/2012 2:22 PM, Nilesh Dhumal wrote:
Hello,
I am trying to run simulation of graphene oxide. I have 16 carbon atoms
of same type. I am using opls force field. could make the .itp file and
pasted here
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
You need to choose some actual values here, not comment them out.
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_071 CG 6 12.01100 0.00 A 3.50000e-01 2.92880e-01
opls_072 CO 6 12.01100 0.265 A 3.50000e-01 3.59824e-01
opls_116 OH 8 15.99940 -0.683 A 3.12000e-01 7.11280e-01
opls_117 HO 1 1.00800 0.418 A 0.00000 0.00000
[ bondtypes ]
; i j func b0 kb
CO OH 1 0.14100 133888.0
OH HO 1 0.09600 231375.0
CG CG 1 0.14000 392459.2 ; TRP,TYR,PHE
CG CO 1 0.14000 392459.2 ; TRP,TYR,PHE
[ angletypes ]
; i j k func th0 cth
CG CO OH 1 90.000 292.880
CO OH HO 1 108.500 230.120
CG CG CG 1 120.000 527.184 ; TYR(OL)
[ dihedraltypes ]
; i j k l func coefficients
; OPLS Fourier function (func=5)
CJ CJ CJ CJ 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
CG CO OH HO 3 0.00000 0.00000 6.27600 0.00000
CG CG CO OH 3 7.15882 -2.09200 2.77399 0.00000
My question how can I step for the parameters ffoplsaa.rtp file. I made
the parameters as follow
[ SMA ]
[ atoms ]
CG opls_071 0.00 1
CG opls_071 0.00 1
CG opls_071 0.00 1
CG opls_071 0.00 1
CO opls_072 0.265 2
CG opls_071 0.00 1
CG opls_071 0.00 1
CO opls_072 0.265 2
CG opls_071 0.00 1
CG opls_071 0.00 1
CG opls_071 0.00 1
CG opls_071 0.00 1
CG opls_071 0.00 1
CG opls_071 0.00 1
CG opls_071 0.00 1
CG opls_071 0.00 1
OH opls_116 -0.683 3
HO opls_117 0.000 4
OH opls_116 -0.683 3
HO opls_117 0.000 4
[ bonds ]
CG CG
CG CO
CO OH
OH HO
You should look at some example .rtp entries. You need to give a unique
name to each atom, and to describe which are bound to which.
Chapter 5 is your friend, read its examples.
Mark
I am geting trouble to create .top file using pdb2gmx.
Can you tell how to set up force field parameter for graphene.
I am usinng Gromacs VERSION 4.0.7.
Thanks
Nilesh
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