[gmx-users] Help! A dummy atom definition problem!

[David van der Spoel]

Wang Qin wrote:
> Hi Maik,
>       I really did mix up a dummy atom with a virtual site. Any difference?
>       Thank you very much for your help.


we changed the name from dummy to virtual site a few years back. We 
didn't want to be associated with MD for dummies.

>  
> Regards,
> Qin
> 
>  
> On 9/12/07, *Maik Goette* <mgoette at mpi-bpc.mpg.de 
> <mailto:mgoette at mpi-bpc.mpg.de>> wrote:
> 
>     The problem actually is, that you mixed up a dummy atom with a virtual
>     site, I guess.
> 
>     Virtual sites are not allowed to have a mass, as the error message
>     claims. Also, a proper hydrogen should have a mass.
> 
>     If you want a hydrogen to appear, you have to place a particle in
>     A-state which has no non-bonded interaction, i.e. LJ & QQ interactions
>     should be zero. If you want to prevent it from flying away, you should
>     put bonded terms to the particle.
>     In the B-state, the QQ and LJ should be there (whereas the LJ
>     interaction for a hydrogen is 0 anyway).
> 
>     21      opls_999        1       LG4     H21     21      0.0000  1.00800
>             opls_172        0.4650  1.00800
> 
>     opls_999   DUM   0     1.008000     0.000    A     0.000000   0.000000
> 
>     So, I expect, this is, how it should look like.
>     Be aware of the missing bonded terms in the force field for a DUM
>     particle. Maybe, you want to call it H instead...
> 
>     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 <http://bpc.mpg.de>
>             mgoette2[at]gwdg.de
>     WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
> 
> 
>     Wang Qin wrote:
>      > Hi there,
>      >        I met the problem when I ran "grompp", the errors are:
>      > ERROR 1 [file "po4lig4tip3.top", line 26741]:
>      >   virtual site H21 (Res LG4-173) has non-zero mass 1.008
>      >        Check your topology.
>      >
>      > ERROR 2 [file "po4lig4tip3.top", line 26741]:
>      >   virtual site H22 (Res LG4-173) has non-zero mass 1.008
>      >        Check your topology.
>      >
>      >       Then I checked my topology file, here were the definition of
>      > LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms)
>      >    ;nr          type    resnr   residue atom    cgnr    charge
>      > mass            type_B  charge_B        mass_B
>      > 21      opls_999        1       LG4     H21     21      0.0000
>      > 1.00800         opls_172        0.4650  1.00800
>      > 22      opls_999        1       LG4     H22     22       0.0000
>      > 1.00800         opls_172        0.4650  1.00800
>      >
>      >        in which opls_999 was from what I defined by myself in the
>     force
>      > field itp file:
>      > opls_999   DUM   0     1.008000     0.000     V     0.000000  
>     0.000000
>      >
>      >       I changed the both of the mass_A to 0.00000, but that
>     didn't help.
>      >       Does anyone have ideas on that?
>      >        Thank you very much.
>      >
>      > Regards,
>      > Qin
>      >
>      >
>      >
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se