Re[2]: [gmx-users] Virtual site and constraints

[Нилов Дмитрий]

I`ve tried to name it like atom (instead of "dummy mass")
in this way:

1)enter new atom type in "ffoplsaa.atp":
 opls_966   12.01100  ; Virtual site in formate

2)enter description of new atom type in "ffoplsaanb.itp":
; name      bond_type  mass    charge  ptype  sigma     epsilon
  opls_966  DF      0  12.011  0.0000  D      0.00e+00  0.00e+00
(also I`ve tried to use "A" instead of "D" in ptype column)

3)correct my topology:
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
     1   opls_279      1    FMT      H      1       0.22      1.008
     2   opls_271      1    FMT      C      1       0.58      0.000
     3   opls_272      1    FMT     O1      1       -0.9    15.9994
     4   opls_272      1    FMT     O2      1       -0.9    15.9994
     5   opls_966      1    FMT      D      1        0.0     12.011

[ constraints ]
;  ai    aj funct    c0
    1     3     2    0.19850
    1     4     2    0.19850
    3     4     2    0.22400

[ virtual_sites3 ]
; Dummy from funct a b
2 1 3 4 1 0.345 0.345
5       1       3       4       1       0.345   0.345

But it does not work because grompp runs with error
"virtual site D (Res FMT-1) has non-zero mass 12.011".
I suppose, that only "dummy masses"(particles named like "M*") could
have mass.
Could you help me, please?
--------------------
Nilov Dmitri  

-----Original Message-----
> Нилов Дмитрий wrote:
> > OK, could I add "dummy mass" that has coordinates and 
> > mass such as carbon to keep right moment of inertia?
> > I mean something like this:
> > [ atoms ]
> > ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> >      1   opls_279      1    FMT      H      1       0.22      1.008   
> >      2   opls_271      1    FMT      C      1       0.58      0.000   
> >      3   opls_272      1    FMT     O1      1       -0.9    15.9994   
> >      4   opls_272      1    FMT     O2      1       -0.9    15.9994   
> >      5         MW      1    FMT      D      1        0.0     12.011
> > 
> > Should I use some constraints for "dummy mass" to define its position
> > in simulation? And can I get "dummy mass" type from ffoplaa.atp or
> > its better to add the new one?
> 
> Have you tried naming it an atom instead of a virtual site?
> > 
> > I`m sorry, I`ve read manual and corresponding article but I have not
> > find irrefragable answer for my questions.
> > 
> > Thanks
> > ------------
> > Nilov Dmitri
> > 
> >  
> >> Нилов Дмитрий wrote:
> >>> Thank you very much, but in what way can I define the carbon
> >>> like massless when it treated as a virtual site(type 3)
> >>> in formate molecule?
> >> You can define it as zero, but take care to get the right moment of 
> >> inertia (by defining further virtual sites).
> >>
> >>> Grompp runs with error when carbon has mass:
> >>>
> >>> converting bonded parameters...
> >>> #  CONNBONDS:   3
> >>> #     CONSTR:   3
> >>> #     VSITE3:   1
> >>> Setting particle type to V for virtual sites
> >>> ERROR 2 [file "fmt.top", line 82]:
> >>>   virtual site C (Res FMT-1) has non-zero mass 12.011
> >>> -----------------------------------------------------       
> >>>
> >>> -----Original Message-----
> >>>> Нилов Дмитрий wrote:
> >>>>> Hello!
> >>>>> I would like to involve formate molecule (HCOO-)in my dynamics, but I have the problem when I use virtual site (type 3fd)for it.
> >>>>>
> >>>>> When I run grompp for single formate molecule, it`s ok.
> >>>>> But after solvating in bath of solvent (tip3p) grompp runs with error:
> >>>> In this case you would be best off defining three constraints from
> >>>> H O1
> >>>> H O2
> >>>> O1 O2
> >>>> and define the carbon as a virtual site defined by the plane (check 
> >>>> TIP4P topology).
> >> -- 
> >> David van der Spoel, Ph.D.