From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Aug 13 2013 - 09:51:30 CDT
Hi Sunhwan,
Thanks for sharing the benchmark figures. One question: are you sure you need to restrain thousands of atoms at a time?
Cheers,
Jerome
----- Original Message -----
> Francesco,
>
>
> I've done testing colvar parallel performance lately, so I'd like to
> share it with you.
>
>
> I've used three systems:
>
>
> #1:
> Total 135K atoms
> 2 RMSD type colvar (1556 backbone and 1561 side chain atoms
> restrained)
>
>
> #2:
> Total 506K atoms
> 2 RMSD type colvar (6224 and 6244 atoms)
>
>
> #3:
> Total 443K atoms
> 2 RMSD type colvar (12448 and 12488 atoms)
>
>
> Each number represents the average (n=3) seconds took to finish 1000
> MD steps staring from restart file.
> These are tested with 8 core machines equipped with infiniband.
>
>
>
>
>
>
> # processor
> #1
> #2
> #3
>
> w/o
> w
> w/o
> w
> w/o
> w
>
> 1
> 1836
> 1845
> 5738
> 5841
> 5180
> -
>
> 8
> 213
> 219
> 798
> 827
> 715
> 829
>
> 16
> 113
> 116
> 433
> 454
> 412
> 485
>
> 32
> 62
> 65
> 225
> 253
> 219
> 415
>
> 64
> 35
> 40
> 132
> 171
> 115
> 370
>
> 128
> 25
> 29
> 87
> 140
> 73
> 352
>
>
>
> Hope this helps.
>
>
> Thanks,
> Sunhwan
>
>
>
>
> On Aug 12, 2013, at 9:54 AM, Francesco Pietra < chiendarret_at_gmail.com
> > wrote:
>
>
> Hello:
> My aim is to carry out parallel tempering of a transmembrane protein
> endowed of peptide ligands in a periodic TIP3 box. I would like to
> restrain all except the mobile parts of the protein. To this end I am
> examining the multifaceted opportunities of colvars with MPI-compiled
> namd2.10.
>
> I would be very grateful for an input on where, in the now quite
> complex panorama of colvars, to concentrate attention in view of the
> above task. My major concern is the large number of atoms to include
> in colvars, which my well conflict with the "few thousand" set fort
> in
> the manual. I.e., ca 20,000 protein + peptide atoms and, if I also
> want to restrain the double-layer membrane, additional 27,000 atoms.
>
> Thanks for advice
>
> francesco pietra
>
>
>
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