[gmx-users] Virtual site and constraints

[David van der Spoel]

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.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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