[gmx-users] Extracting protein plus a shell of water from a .xtc file

Paolo Conflitti paolo.conflitti at gmail.com
Mon Nov 15 16:30:50 CET 2010

Dear gmx-users,

  I'm trying to extract a protein plus a shell of water of a given 
radius from the .xtc and .gro files obtained from a simulation step. My 
purpose is to make a second box, smaller then the first, with the 
protein and the shell of solvent in order to optimize the performance of 
the simulations that I'm running (they require an incredible amount of 
time due to the high number of H2O molecules in the box) and retain the 
data obtained till now without starting a new run from the beginning.
  I've tried to use trjorder with the command -o .pdb -nshell .xvg -r 
x.x and I've obtained a .pdb file with the distances of the molecules of 
water from the protein (reference group: Protein, group of molecules to 
be ordere: SOL) printed in the B-factor field.
  Now I'm going to modify the pdb file removing all the molecules that 
are too far from the protein. I will use this file to make a second box, 
add the water needed to fill it and restart the simulation.
  I'm concerned about this procedure because I'm afraid that I'll 
introduce some errors in the new run, so I wonder if there's a faster 
way to achieve the same result. I've tried different ways, even using 
other softwares (e.g: MolMol), but I have not been able to extract the 
shell of water.
  If there's no other way to do this, could someone please give me a 
hint about the procedure I'm attempting on?
  Thanks in advance for your attention and patience.


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