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.
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