[gmx-users] deletion of some water molecules

[Erik Marklund]

  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/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100831/137ce41b/attachment.html>