[gmx-users] default group question

David spoel at xray.bmc.uu.se
Mon Nov 10 20:27:01 CET 2003

On Mon, 2003-11-10 at 17:05, qiao rui wrote:
> Hi, there:
> 	I am doing a simulation in which I wish to monitor the diffusion
> of water molecules in my system. To this end, I have the following
> topology file:
> 	...
> 	SOL	100
> 	LOL	100
> 	HOL	100
> 	...
> 	SOL/LOL/HOL are all water molecules, I define their residue name
> in such a way to distinguish the water molecules in different part of the
> system.
> 	In using Gromacs, I first find that the default group shows SOL
> only, but not LOL and HOL (why?) To solve this, I defined an index file,
> where LOL and HOL are defined. However, after I did an energy
> minimization, the output .gro file has only SOL - the name of LOL and HOL
> molecules was changed to SOL (all the LOL and HOL waters are still
> their, but their name was changed to SOL somehow). Why is this happening?
It uses the residue name in the topology. You can however stil use your
index file.

> 	Thanks a lot for your input.
> 	sincerely,
> 	Rui
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David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel

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