Dear all gmx-users,
I have recently been testing the REMD simulations. I was running simulations on a supercomputer system based on the AMD Opteron 12-core (2.1 GHz) processors. The Gromacs 4.5.3 version was used. I have a system of 5172 atoms, of which 138 atoms belong to solute and the other are water molecules. An exponential distribution of temperatures was generated ranging from 276 to 515 K in total of 42 replicas or from 298 to 420 K in total of 24 replicas, ensuring that the exchange ratio between all adjacent replicas is about 0.25. The replica exchange was carried out every 0.5ps. The integrate step size was 2fs. For the above system, when REMD is simulated over 24 replicas, the simulation speed is reasonably fast. However, when REMD is simulated over 42 replicas, the simulation speed is awfully slow.Please see the following table for the speed. ---------------------------------------------------------------------------- Replica number CPU number speed 24 96 58015steps/15minutes 42 42 865steps/15minutes 42 84 1175steps/15minutes 42 168 1875steps/15minutes 42 336 2855steps/15minutes The command line for the mdrun is: aprun -n (CPU number here) mdrun_d -s md.tpr -multi (replica number here) -replex 250 My questions are : 1) why the REMD for the 42 replicas is so slow for the same system? 2) On what aspects can I improve the operating efficiency please? Many thanks in advance for your help! Qiong ZhangDepartment of Theoretical Chemistry School of Biotechnology Royal Institute of Technology Roslagstullsbacken 15 SE-10691 Stockholm, Sweden Tel: +46 855378422 E-mail: zh...@theochem.kth.se
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