Sorry Marcelo, that sounds like a job for an author ;) If nobody else
chimes in, then I suggest that you do some testing and come back to
the list with specific problems. As an analogy, you might look at how
the virtual site is handled in tip4p in the absence of settle.
Chris.
-- original message --
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?) ;
* 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?
4) The virtual site in the COM is [ virtual_sites2 ] with a = 0.5 or [
virtual_sitesn ]?
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