[gmx-users] Add gromacs forcefield w/ virtual site

[Mark Abraham]

On 31/12/2010 5:03 AM, Marcelo Silva wrote:
> Thank you Chris for your answer:
>
> 1) The molecule has no net charge because the virtual site in the 
> center of mass is a point charge twice the charge in the O atom.
> 2) Until now I've created 5 files but I don't know if I am doing the 
> right thing:
>
>     *  forcefield.itp
>
> #define _FF_OXY
>
> [ defaults ]
> ; nbfunc        comb-rule         gen-pairs        fudgeLJ     fudgeQQ
> 1                    2                        no                    
> 1.0            1.0
>
> #include "ffnonbonded.itp"
> #include "ffbonded.itp"
>
>     *   ffbonded.itp
>
> [ bondtypes ]
> ; i    j       func
>   O    O         5  (I've used function 5 because the forcefield has a 
> fixed length, is it right?) ;

If the bond length is to be fixed, then you want constraint type 1. Bond 
type 5 has a different application.

>
>     *   ffnonbonded.itp
>
> [ atomtypes ]
> ; name  at.num        mass              charge   ptype              
> sigma          epsilon
>      O                8       15.99940        -0.123       A         
> 3.01300e-01    4.0780822e-01
>    COM            0       0.000000         0.246       V         
> 0.00000e+00    0.0000000e+00
>
>     *  atomtypes.atp
>
> O     15.99940  ; Oxygen Atom
> COM   0.0       ; Virtual site (COM charge)
>
>     *  residues.rtp
>
> ; Oxygen
> [ OXY ]
>  [ atoms ]
>      O         O              -0.123    1
>      COM   COM        0.246    1
>  [ bonds ]
>     O    O
>
> 3) Is it necessary more or less files? And in which file do I 
> specificate de virtual site?

Virtual site directives are listed in Table 5.6, so they need to end up 
in the [moleculetype], which means they need to be in the .rtp entry. 
Some of the forcefield files probably have examples of this.

> 4) The virtual site in the COM is [ virtual_sites2 ] with a = 0.5 or [ 
> virtual_sitesn ]?

I guess either would work, but the former is simpler.

Mark
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