[gmx-users] LINCS error

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 31 23:07:54 CEST 2008

sarbani chattopadhyay wrote:
>   Hi,
>     I am trying to simulate a peptide whose structure is yet to be 
> validated experimentally.
> It has 3 protonated lysine residues.
> I have used "oplsaa" force filed with "spc" water model and had added 3 
> CL ions into the box.
> Everything works fine till energy minimisation but after that during 
> position restricted dynamics, I encounter segmentation fault that states
> "relative constraint deviation after LINCS:"
> I again energy minimized the structure and then during the position 
> restrained dynamics run I get the error
> "Can't settle water molecule starting with .."
> While going through the "Suggestions for creating helix in octane 
> simulation system in gromacs" I got the suggestion to remove that 
> particular water molecule from the starting configuration and energy 
> minimising it again.
> I removed the molecule from the already energy minimised structure, 
> updated the topology file and again ran the position restrained 
> dynamics. But again the same error comes that a particular water 
> molecule can't be settled.
> I had tried to use different energy minimisation processes but still I 
> am unable to fix this problem

Have you tried searching the archives for other solutions?  Searching for 
"cannot settle water molecule" and "LINCS warning" together return almost 600 
results.  This is probably one of the most common problems reported to this list.

Deleting the problematic water molecule is almost never the solution.  For some 
more reference, see here:


Visualize the trajectory, see where things are blowing up, and re-evaluate what 
you are doing.


> If I get any help , it will be highly beneficial.
> Sarbani
> Ebay 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null>
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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