[gmx-users] Virtual site and constraints

[Maik Goette]

Virutal particles should not have any mass.
Its, e.g. for placing a delocalized charge (as in TIP4P) somewhere.
How about carefully reading the warnings and try to do, what they suggest?
How about this?:
 >      5   opls_966      1    FMT      D      1        12.011    0.0

Now you have a charge there and no mass. Thats, how virtual sites work.
If you want to use a "free energy dummy", you may have to use a 
different approach.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Нилов Дмитрий wrote:
> 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.
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> .
>