Hello,
1)I am currently working on DS 2016. I ran a 2ns simulation consisting of 1000 frames using NAMD protocol. the simulation went just fine. when I analyze the trajectory for RMSD (main chain atoms), the protocol runs for about 5 hours then fails with this message : "GC overhead limit exceeded"
2)I ran a different simulation with truncated octahedron solvation box, it runs perfectly using the standard dynamic cascade but fails directly using NAMD with the message PME nneds periodic boundry
1)I am currently working on DS 2016. I ran a 2ns simulation consisting of 1000 frames using NAMD protocol. the simulation went just fine. when I analyze the trajectory for RMSD (main chain atoms), the protocol runs for about 5 hours then fails with this message : "GC overhead limit exceeded"
2)I ran a different simulation with truncated octahedron solvation box, it runs perfectly using the standard dynamic cascade but fails directly using NAMD with the message PME nneds periodic boundry
