[gmx-users] Gromacs on Gigabit Ethernet Dual Opteron Cluster

Ghermes Chilov Ghermes at belozersky.msu.ru
Mon Oct 6 11:23:01 CEST 2003

Hello Anton,

Monday, October 6, 2003, 11:59:40 AM, you wrote:

AF> Ghermes Chilov wrote:
>> The system (dummified protein in water)is big enough:~ 107.000 atoms,
>> -shuffle -sort were used.

AF> If your protein is big w/r the number of waters, it will become limiting
AF> as soon as it fills a whole processor, i.e. CPU0 will be overloaded with
AF> protein, and the others are doing water with time to spare...

No, it's not big: ~ 7-8% of the system... khmm, it becomes sufficient
for 100%/8%=12 CPU's, isn't it?  Or even for a smaller number, if
water-water interactions are in principle more easy to calculate.


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