[gmx-users] dummies

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Sep 7 10:47:10 CEST 2005


I see, but where did you get the definition file with dummies from, then??
Nevertheless, one idea to let the dummy position generation happen 
automatically would be to take the parameters of your topology file as 
"border conditions" for dummy atom positions and then place a particle 
in a position inside these borders...the equilibration should be enough 
to place them properly.

Someone mentioned, that theres a switch in the source code, to switch of 
the quotes...but I don't know where...


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

Omololu Akin-Ojo wrote:
> Hi Maik,
> thanks for the response.
> To make things clearer:
> my pdb file did *not* contain the dummies, but only
> the real atoms. if you download a *.pdb file from the
> pdb, it does not conatin dummy atoms.
> my force field for the non-bonded interaction uses
> dummies. My molecule definition (*.itp) also contains
> the dummies.
> i was hoping i would not have to manually put the
> dummy atoms in the *.pdb file. Afterall, from the
> molecule definition it is possible to generate the
> posions of the dummies. i already did it manually any
> way.
> someone helped me to customize the gurgle.dat file --
> ngmx does not work with the new gurgle.dat but i have
> vmd and rasmol to visualize anyway.
> i agree they are just quotes, but i don't appreciate
> the 'f' word, for example on my computer. i'm not
> saying to turn it off for all users, but i just wanted
> mine off.
> Cheers,
> o.
> --- Maik Goette <mgoette at mpi-bpc.mpg.de> wrote:
>>I don't understand your question, it seems.
>>If your forcefield-files contain dummy atoms, the
>>topology file still 
>>doesn't. And thats also true for the gro-file.
>>If you want to use dummies, they have to be included
>>in the pdb-file, or 
>>you have to add them manually in the gro-file and
>>the topology later.
>>GROMACS is a really fine tool, but the
>>isn't included yet...
>>The way to use GROMACS best is:
>>pdb2gmx with your PDB-file (including Dummies)
>>then, you get the topology and the gro-file
>>(including dummies).
>>Then use editconf to generate the box, fill it with
>>water by genbox and 
>>add counter ions...then use grompp to generate your
>>Even, if you have a topology file with dummies,
>>GROMACS needs the 
>>positions of the dummies and they are in the
>>gro-file. If you don't have 
>>any dummy-positions, just parameters for bonds,
>>etc., GROMACS can't 
>>guess them, I suppose.
>>The quotes are just quotes...first, I think no one
>>really cares about 
>>them and second: I you don't like them, don't use
>>Maik Goette, Dipl. Biol.
>>Max Planck Institute for Biophysical Chemistry
>>Theoretical & computational biophysics department
>>Am Fassberg 11
>>37077 Goettingen
>>Tel.  : ++49 551 201 2310
>>Fax   : ++49 551 201 2302
>>Email : mgoette[at]mpi-bpc.mpg.de
>>         mgoette2[at]gwdg.de
>>WWW   :
>>Omololu wrote:
>>>i am new to gromacs. i must say thanks to the
>>>developers of this program. it's simply great!
>>>1) my *.pdb file does not contain dummy atoms
>>>(dummies) but my forcefield does. In my *.itp
>>file, i
>>>put the definition for all atoms including the
>>>dummies. i used "editconf" to get a *.gro file but
>>>this does not contain the dummies. How can i use
>>>program "grompp" without getting errors since
>>>are dummies in my *.itp file which are not in
>>>i hope i do not have to edit the *.pdb file and
>>>the dummies in there.
>>>2) is there a way to turn of the silly quotes that
>>>programs write when they finish? Some of them seem
>>>be quite offensive. I tried getting rid of the
>>>"gurgle.dat" file but then "ngmx" crashes when i
>>>to use it. Or is there a way to create my own
>>>thanks a lot for any help.
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