[gmx-users] Water atoms cannot be settled

[Ms. Aswathy S]

Hi ,

I am doing a protein ligand Md simulation.

1. I did the energy minimization
2. A 500 ps NVT equilibration
3. then a 1 ns NPT simulation , and seemed that the system is equilibrated enough I went ahead with Md run for 5 ns.

But at the step of 70000 I got the error like "Some of the water atoms cannot be settled." I understood that some water molecules making bas contacts/ or clashes. But How can I rectify that ? Do I need to continue with equilibration again? or any tother way to get out of this problem"?

Attaching the equilibration parameter files here with .
Please tell me your comments, Thanks
Aswathy
Dept. Biotechnology
Ext. 3108
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