[gmx-users] LINCS warnings

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 11 12:28:00 CEST 2012

On 6/11/12 6:23 AM, rama david wrote:
> Hi Mark,
> I did simulation of the same system in vacuum, and system behave the normally,
> So the instability  in the system is due to the spc Water model???
> As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up

The water model is not the problem.  Your solvated system has clashes that cause 
instability.  In vacuo, your solute has greater freedom to shift around.

> I think the source is (Please tell me is it right..?? or any else reason  )
> last option :
> you have a single water molecule somewhere within the system that is isolated
> from the other water molecules.
> How to find such water molecule and solve the problem??

I think this is unlikely.  If you have any isolated waters, they might be 
sandwiched somewhere in your protein layers and should be easy to spot.  The 
best strategy is to use the output of EM to your advantage.  Look at the atom 
that had the highest force on it.  What is it near?  What might it be clashing 
with?  What if you run EM in vacuo, followed by solvation, and another round of 

 From your earlier description, it seems to me that the system has been 
constructed to replicate some known experimental spacing, but doing so does not 
guarantee that whatever peptide structure you are replicating will necessarily 
produce a sensible result, or one that is free from clashes.  Hence, you need to 
refine the model before continuing.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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