[gmx-users] default group question

[qiao rui]

Thanks David,

I checked my .top file, and the residue name there is
SOL/LOL/HOL instead of just SOL.

sincerely,

Rui
------------------------
Rui Qiao
Research Assistant
Beckman Institute, UIUC

On 10 Nov 2003, David wrote:

> 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.
> ________________________________________________________________________
> 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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