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 <[EMAIL PROTECTED]> 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
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3584 CH Utrecht
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