[gmx-users] LINCS error

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Sun Aug 31 19:27:21 CEST 2008

     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

If I get any help , it will be highly beneficial.
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