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
md_Eq1_NVT.mdp
Description: Binary data
md_NPT.mdp
Description: Binary data
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