[gmx-users] deletion of some water molecules

Erik Marklund erikm at xray.bmc.uu.se
Tue Aug 31 14:52:49 CEST 2010

  leila karami skrev 2010-08-31 14.48:
> Dear gromacs users
> I did simulation of protein-dna complex in a box with size 7,7,7. 
> There are 5000 water molecule in this box. After full md simulation, I 
> need a pdb or gro file containing only water molecules being exactly 
> environment of pr-dna complex and not water molecules being in edges 
> or rest of box.
> Is there any way to do that?
Use trjorder which orders your water molecules according to their 
distance to the solute. Then remove tha last few thousand waters in a 
text editor.

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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