From: Sunhwan Jo (sunhwan_at_uchicago.edu)
Date: Mon Aug 12 2013 - 10:29:23 CDT
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<mailto: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
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:33 CST