[gmx-users] default group question

qiao rui ruiqiao at glsn12.ews.uiuc.edu
Mon Nov 10 17:06:04 CET 2003

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
	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?

	Thanks a lot for your input.



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