[gmx-users] centering

[Anton Feenstra]

Marc Vogt wrote:
> I tried
> editconf -f start.pdb -o centered.pdb -center 2.5 2.5 2.5
> and 
> editconf -f start.pdb -o centered.pdb -c
> 
> and different versions of gromacs but the resulting centered.pdb always 
> looks like the starting one.  Seems like it should be easy and I'm sure
> it's something stupid, but I can't get it.

I don't think editconf has the periodic boundary options that you'd need 
for this. In stead you could use trjconv (try 'trjconv -h' and look for pbc).

Something like 'trjconv -f centered.pdb -s centered.pdb -o pbcinbox.pdb 
-pbc inbox' could work (check the options etc.)

(Maybe trjconv vcan do the centering as well, I'm not sure...)

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
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