[gmx-users] freeze water

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 28 20:02:56 CEST 2006

Anthony Cruz wrote:
> Hi:
> I want to make a simulation of a small pepetide in a box of water but I want 
> to freeze or restrain the movement of all water molecules that have a 
> distance grater that 3 A from the protein surface.  Right know the water that 
> are within 3 A of the protein, have a different residue name (SHL) and the 
> other water molecules have the normal resname (SOL)  How I could do the 
> restrain??? 
use make_ndx to make an index file and freeze all SOL
> Thanks.
> Anthony 
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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