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

[Mark Abraham]

ucsd mail wrote:
> 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. 

You cannot have a bonded interaction between atoms that belong to
different [ moleculetype ] directives. So you will need to make a hybrid
of the nanotube and the polymer. Depending on what sense you think it
will be "better" to have them as separate molecules, you may wish to
define index groups with make_ndx for whatever use you have in mind.

Mark

> 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
> 
> 
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> 
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