<P>
Hi,<BR>
I am trying to simulate a peptide whose structure is yet to be validated experimentally.<BR>
<BR>
It has 3 protonated lysine residues. <BR>
I have used "oplsaa" force filed with "spc" water model and had added 3 CL ions into the box.<BR>
Everything works fine till energy minimisation but after that during position restricted dynamics, I encounter segmentation fault that states<BR>
"relative constraint deviation after LINCS:"<BR>
I again energy minimized the structure and then during the position restrained dynamics run I get the error<BR>
"Can't settle water molecule starting with .."<BR>
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.<BR>
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.<BR>
I had tried to use different energy minimisation processes but still I am unable to fix this problem<BR>
<BR>
If I get any help , it will be highly beneficial.<BR>
Sarbani<BR>
<BR>
</P>
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