[gmx-users] protein+2water molecules

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 13 09:56:20 CET 2001

On Tue, 13 Nov 2001, Dmitry Kovalsky wrote:

>Hi All,
>Is it possible while converting trajectory from trr to xtc (or any other format, using trjconv)  to obtain protein plus few water molecules which are of my interest. I mean that there are 2 water molecules in active site which trajectory is important for me and I want to see them in my trajectory after removing the bulk solvent molecules. Or another way like this: to create a sphere with definable center and radius (for example with its center  in the center of active site). All solvent molecules which are within the shpere become visible in converted trajectory. 
Yes, just make an index file with the group you want to select.
Use the make_ndx tool to do this.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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