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.
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-----------------------------------------------
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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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