[gmx-users] Re: parallel mdrun (mpimdrun) is slower than

[Vitaly Chaban]

>  I am performing a MD simulation of a polymer film using GROMACS-4.0.7. My computer has a four-core CPU, which enables the parallel implementation. At first, I used mpimdrun to simulate the system, only to find with -v that the vol is too small (about 0.2) and the imb F is too big (over 150%) so about 4 days is required for finishing 4ns MD. However, when I turn to non-parallel mdrun, only half of the time (about 2 days) is required for finishing the same task. Is it reasonable? How to explain it?

Very easily. You have a small polymer in the system.

Dr. Vitaly Chaban