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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