[gmx-users] Dummies usage doubts

[David van der Spoel]

Jones de Andrade wrote:
> Hi all.
> 
> Well, I'm having a bit of trouble here because the work has decided to 
> go in the direction of something I've never used before with gromacs: 
> dummy atoms (or now "virtual sites").

I assume this is not for a protein, in which case pdb2gmx does it for you.
> 
> I've got at least three questions in order to use them:
> 
> 1 - does the virtual sites need to be included in the .gro files in 
> order to make a simulation run?
> 
Yes.

> 2 - do I need to include them in the "exclusion list"?
It depends, but usually yes.

> 
> 3 - do I need to include them in the "atoms" section?
Yes.

> 
> 
> Thanks a lot in advance for any help anyone can provide in these 
> subjects. ;)
Check the mannual too. Chapter 5. An dtopologies for TIP4P, TIP5P etc.


> 
> Sincerally yours,
> 
> Jones
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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