[gmx-users] Why REMD simulation becomes so slow when the number of replicas becomes large?

Qiong Zhang qiongzhang928 at yahoo.com
Mon Feb 7 11:52:26 CET 2011

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

96             58015steps/15minutes

42             865steps/15minutes

84             1175steps/15minutes

168             1875steps/15minutes

42                          336            2855steps/15minutes


The command line for the mdrun

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: zhang at theochem.kth.se

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