ADL: Could I run more than one docking at the same time??

L. Michel Espinoza-Fonseca mef at
Mon Apr 13 13:54:00 PDT 2009

A couple of comments below.

> people use to perform embarrassingly parallel procedures to perform VHTS since
> 1) using only one single CPU to screen millions of compounds would take thousands of years of calculations.

This is not necessarily true. With the advent of new algorithms you
can efficiently perform docking simulations in seconds. Things get
even better If you have access to multi-core machines, where you can
perform several individual docking simulations simultaneously (this
comment is also meant as a reply to the original message by Mostafa).

> 2) MPI communications affect the scaling when using more than 8000 CPUs (average).

Again, this will depend on the program you are using. To date, it
seems meaningless to use thousands of processors for a single docking
simulation, as usually one can efficiently run a single docking job on
a single core. This comment will definitively be appropriate for
computationally intensive algorithms, like molecular dynamics
simulations of systems with several thousands of atoms.

> Barbara
> ge-----
> From: autodock-bounces at on behalf of Daniel Jana
> Sent: Mon 4/13/2009 3:17 PM
> To: autodock at
> Subject: Re: ADL: Could I run more than one docking at the same time??
> Hello Mostafa,
> Mostafa El-Miligy wrote:
>> Could I run more than one docking at the same time without any problem??
> Computer programs don't mess up their paperwork as humans do. As long as
> you keep things separate (different files, possibly, different folders)
> things should work fine. Just remember that you don't get much
> performance out of running tons of simulations a single cpu...
> Best,
> Daniel
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