[gmx-users] lipid solvent

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue May 15 20:32:56 CEST 2007

I don't really understand what you are trying to do, but one thing  
that popped to mind is that if your current system is current.gro you  
can do this:

genbox -cp empty_file_with_box_dimensions_I_want.gro -cs current.gro

Basically you are "solvating" an empty box with replicas of your  
system. If your system if larger than the box then only part of your  
system will be included in the output.

Probably you can trjconv -translate your current.gro and repeat genbox  
to get the output you desire (although I am not sure about that one).

I do this for example if I have some waters that are too close to the  
protein in an erroneous setup (or recently as output from an  
improperly completed make_hole mdrun of a collegue) then I strip out  
the waters into a seperate file of exactly the same size and then use  
then to resolvate via genbox.


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