[gmx-users] Virtual sites parameters

[Justin Lemkul]

On 6/18/13 12:20 PM, Bastien Loubet wrote:
> Dear GROMACS user,
>
> I have been trying to define parameters for virtual sites in CHARMM lipid,
> and I would like to know if there is something simillar to the [ bondtypes ]
> for virtual sites.
> Specifically the way I specify the parameters now is by having lines in the
> topology such as (for a 3fout virtual sites):
>
> [ virtual_sites3 ]
> ;  ai    aj    ak    al funct            c0            c1            c2
>     40    39    37    51     4     -0.26909  -0.26909  4.5519
>
> But then I have to do that for every virtual sites in the molecule, even if
> the parameters are the same.
> What I would like to be able to do is:
> [ XXXX ]
> ;  ai    aj    ak    al funct            c0            c1            c2
>     H     C     C    C     4     -0.26909  -0.26909  4.5519
>
> and then
> [ virtual_sites3 ]
> ;  ai    aj    ak    al funct            c0            c1            c2
>     40    39    37    51     4
>
> Where atom 40 is of type H and atom 39, 37 and 51 of type C and XXXX should
> be are directive similar to [ bondtypes ] but for virtual site.
> Does this XXXX directive exist ? I had no luck checking the manual.
>

Not likely, because virtual sites aren't generally built based on types, but 
based on specific atoms.  The workaround that came to mind is to make use of 
#define macros, like how the Gromos96 force fields define bonded terms.  You can 
simply:

#define param -0.26909 -0.26909 4.5519

Then, for your virtual sites:

[ virtual_sites3 ]
;  ai    aj    ak    al funct            c0            c1            c2
    40    39    37    51     4   param

Not quite as efficient as defining types, but since that's not an option, it 
does save some typing.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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