[gmx-users] removing a water molecule

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 28 19:29:13 CEST 2007

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



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
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