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
--
========================================
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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