[gmx-users] Virtual sites parameters

Bastien Loubet bastien at memphys.sdu.dk
Tue Jun 18 18:20:36 CEST 2013

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.

Best regards,

Bastien Loubet

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