[gmx-users] Re:200 CPU, 3ns/day for 80,000 atoms

[Mark Abraham]

On 29/03/2012 11:03 AM, Dr. Vitaly V. Chaban wrote:
>>   I am using gromacs for membrane simulation (under CHARMM36 FF) which
>> contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
>> for such system with 2 fs time step. And what really astonished is that the
>> efficiency for such simulation is only 3ns/day..... I am wondering what
>> happen to my system or gromacs? What can I do to fasten the simulation?
>>
>> here is my md.mdp:
>> *
>> title                    = god!
>> cpp                      = /usr/bin/cpp
>> include                  =
>> define                   =
>> integrator               = md
>> dt                       = 0.001
>> nsteps                   = 100000000
>> nstxout                  = 1000000
>> nstvout                  = 1000000
>> nstlog                   = 1000000
>> nstenergy                = 10000
>> nstxtcout                = 100000
>> xtc_grps                 =
>> energygrps         = Protein POPC SOL ION
>> nstcalcenergy            = 1

I agree with the other thoughts mentioned, and would add that 
nstcalcenergy = 1 triggers global communication every integration step, 
and that is increasingly inefficient at high parallelization.

Mark