[gmx-users] default group question

[David]

On Mon, 2003-11-10 at 21:13, qiao rui wrote:
> Thanks David,
> 
> I checked my .top file, and the residue name there is
> SOL/LOL/HOL instead of just SOL.
Residue name or molecule name?

> 
> 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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> 
> 
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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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