[gmx-users] removing a water molecule

Ragothaman Yennamalli ymr79in at yahoo.co.in
Tue May 29 05:56:20 CEST 2007


Hi,
Thanks for the mail. I checked my input structure. I
dont have any water along with the protein.
Regards,
Ragothaman

--- Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ragothaman,
> 
> Also check for isolated water molecules. These can
> be a pain, since
> they are sort of part of the protein, but are
> coupled to the solvent
> outside. One common source for
> LINCS/water-molecule-can't-be-settled
> errors.
> 
> Cheers,
> 
> Tsjerk
> 
> On 5/28/07, Mark Abraham <Mark.Abraham at anu.edu.au>
> wrote:
> > Ragothaman Yennamalli wrote:
> > > Thanks.
> > > I do get LINCS warning all the time. I had
> removed two
> > > water molecule, that seemed too close to where
> the
> > > LINCS warning came for. And started the
> simulation
> > > again from the scratch and it stopped as
> mentioned in
> > > my previous message.
> >
> > Yup. Go and fix your equilibration regime (copy
> something reasonable
> > from a published paper or a tutorial). A normal
> simulation should have
> > no LINCS errors.
> >
> > Mark
> > _______________________________________________
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> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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