[gmx-users] Water residence time

David spoel at xray.bmc.uu.se
Tue May 6 22:37:01 CEST 2003

On Tue, 2003-05-06 at 19:10, Andrea Bernini wrote:
> Dear gmx users,
> 	I would like to compute residence time of water molecules on a protein 
> surface using a md trajectory of a solvated system. Is it possible to 
> carry out such calculation using Gromacs tools?
Yes, check out g_hbond. You'll have to do it in two steps.

> If not, is it possible to obtain a list of water molecules that are 
> closer than a given distance to the protein for each frame?
Yes, using trjorder

> Thanks in advance, Andrea.
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel

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