[gmx-users] topology info for specific bond between atoms in different molecules

[ucsd mail]

Hi There,

I am a new user of Gromacs and want to work on carbon nanotubes. 
I want to simulation carbon nanotube(cnt) bonded with polymers in water. And it will be much better to consider cnt and the bonded polymer as separate molecules, instead of one molecule.  I can create the .itp file for both the nanotube and the polymer chain, and include them in the .top file. But I do not know how to describe the bond betwen the cnt and the polymer. 
Currently my .top file looks like this: (Thanks a lot!)
*******************************************
[ defaults ]
; nbfunc    comb-rule    gen-pairs  fudgeLJ   fudgeQQ
       1            1 

[ atomtypes ]
; type     mass   charge ptype      c6             c12
     C     12.0      0.0   A        0.0            0.0
     X    1.0e10     0.0   A        0.0            0.0
    OW    15.994    -0.82  A        0.0            0.0
     H     1.008     0.41  A        0.0            0.0
     ...more info

[ nonbond_params ]
;     ai    aj   funct   aij             bij
  C     C      1    2.8768001E-3        4.691598E-6 
 OW    OW      1    2.6169064E-3        2.633236E-6
  C    OW      1    1.3176287E-3        1.388472E-6
  ...more info

[ bondtypes ]
; i   j  func  b0  kb  beta
  C   C     3  0.1418  478.9  21.867 
  ...more info

[ angletypes ]
;i  j  k  func  th0  cth
 C  C  C     2   120.0  562.2
 ...more info

[ dihedraltypes ]
; i     j    func   phi0   cp       mult
  C     C     1     180.0    12.56    2
  ...more info

#include "cnt_test.itp"
#include "FLEXSPC.itp"
#include "polymer.itp"

[ system ]
CNT_H2O

[ molecules ]
CNT   1
SOL   1419
POL   2
*********************************************

I read the manual and found an example that include bonds in topology file like below. The atom IDs are specified instead of atom type. Can I do this for atom (ID) in different molecules? Thanks.
*********************************************
[ bonds ]
; ai aj funct b0 kb
3 4 1 1.000000e-01 3.744680e+05
3 5 1 1.000000e-01 3.744680e+05
6 7 1 1.000000e-01 3.744680e+05
6 8 1 1.000000e-01 3.744680e+05
1 2 1 1.230000e-01 5.020800e+05
1 3 1 1.330000e-01 3.765600e+05
1 6 1 1.330000e-01 3.765600e+05
*************************************************

Regards,
Stone
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090804/fedf238e/attachment.html>