[Dock-fans] Errors in running DOCK6 MPI

Julio Dominguez acheron24 at hotmail.com
Tue Jun 14 14:10:56 PDT 2016


>From the manual:
If the HA_RMSDs is "-1000.0", then there is an inconsistency in the number of heavy atoms between the reference and the docked conformer.
But as to the difference for using the two different .in I don't know. However, it might be related to the core use. How many ligands are you docking?As far as I remember, running dock in mpi only improves the docking of several ligands at once, not the performance of one.
That being said, I have seen very different performances when running dock in AMD vs Intel.
I hope this helps.

> From: thanh.q.le at sjsu.edu
> Date: Tue, 14 Jun 2016 14:00:47 -0700
> To: dock-fans at docking.org
> Subject: Re: [Dock-fans] Errors in running  DOCK6 MPI
> 
> I forgot to mention one thing, this error can only be seen while using DOCK6 MPI fix.in; regular dock6 flx.in does give the desired numbers.
> Thanh Le
> > On Jun 14, 2016, at 1:53 PM, Thanh Le <thanh.q.le at sjsu.edu> wrote:
> > 
> > Hi,
> > The result I received after running dock6 MPI flx.in seems really off:
> > ########## HA_RMSDs:		-1000.0000
> > ########## HA_RMSDh:		-1000.0000
> > ########## HA_RMSDm:		0.0000
> > ########## Cluster Size:	1
> > ##########    Grid Score:         -246.470337
> > ##########      Grid_vdw:         -111.281166
> > ##########       Grid_es:         -135.189178
> > ##########    Int_energy:           52.528397
> > I would like to know why I got -1000.0000 for both HA_RMSDs and HA_RMSDm and 0 for HA_RMSDm.
> > Also, when using dock6 mpi on a cluster (64 cores), the program runs slower than a single core-must be more than 10 times slower.
> > Please help,
> > Thanh Le
> 
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