[gmx-users] protein-SWCNT md simulation

[Atila Petrosian]

Dear Justin

Thanks for your reply.

>  2. Create topology for other elements using g_x2top or other external software
and convert them to .itp

Can I use PRODRG server to creat topology for cnt?

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Parameters of amber 03 which I used are as follows:


ffcnt.atp file >>>

CA                12.01000	; sp2 C pure aromatic (benzene)


ffcnt.n2t file >>>

C    CA    0.00    12.01000  3    C 0.141   C 0.141   C 0.141
C    CA    0.00    12.01000  1    C 0.141


forcefield.itp file >>>

#define _FF_cnt
[ defaults ]
; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
1	2	yes	1.0	1.0

#include "ffcntnonbon.itp"
#include "ffcntbon.itp"


ffcntbon.itp file >>>

[ bondtypes ]
; i	j	func	b0	kb
CA  CA         1    0.14000   392459.2

[ angletypes ]
; i	j	k	func	th0	cth
CA  CA  CA           1   120.000    527.184

[ dihedraltypes ]
; i	j	k	l	func   phase      kd      pn
CA  CA  CA  CT       4      180.00     4.60240     2


ffcntnonbon.itp file >>>

[ atomtypes ]
;name	at.num	mass	charge	ptype	sigma	epsi
CA           6      12.01    0.0000  A   3.39967e-01  3.59824e-01

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Please check content of these file. If there is problem, please tell me.

Best wishes