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

[Нилов Дмитрий]

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?

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.