Re: colvars and parallel-tempering with namd2.10

From: Sunhwan Jo (sunhwan_at_uchicago.edu)
Date: Tue Aug 13 2013 - 10:29:08 CDT

I was curious about the parallel performance of Colvar. But I could certain think of a case where I would like to restrain thousands of atoms at a time.

Another performance problem of colvar is inability to scale when large number of colvars are applied, which is desirable during equilibration of crowded system, e.g., systems containing unsaturated lipids, lipids in general, and carbohydrates.

Best,
Sunhwan

On Aug 13, 2013, at 9:51 AM, Jrme Hnin <jerome.henin_at_ibpc.fr>
 wrote:

> 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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