[gmx-users] Performance loss during pulling simulation

[Jan Meyer]

Dear gromacs user,

i am running a system consisting of two silica-clusters (~3000 Atoms)  
who are surrounded by 85 polymer
chains. Each polymer chain contains 200 monomer-units. The overall  
number of atoms is roughly 10^5. During the simulation i fix one of  
the clusters. The other one is
pulled towards the fixed one. When i run this pulling simulation for  
T=300 K i get  a performance of ~6.5 ns/day. Increasing
the temperature to 400 K leads to a performance of ~3.0 ns/day. This  
effect seems to be systematic for all the simulations i am doing on  
these and similar systems.

I wonder where this performance loss comes from. So far i think it has  
to do with the pulling because i dont see this difference in  
performance doing equilibrium simulations.

I would be greateful for any  explanations or suggestions to fix this.

Best regards,
Jan