Hi,
Try the OpenMP version of cpptraj (cpptraj.OMP) - the 'radial' command
is OpenMP-parallelized. If you have access to multiple compute nodes
you can also compile a hybrid MPI/OpenMP version of cpptraj which will
allow you to split the trajectory read across several nodes, resulting
in further speedup. Making the hybrid version is currently only
possible using cpptraj's own configure script.
-Dan
On Wed, Jun 1, 2016 at 1:28 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Dear List,
>
> I have ~28000 waters in a system with protein-ligand embedded in the
> bilayer. I am trying to calculate rdf with specific atom of the ligands (N,
> COO-) and H1 of waters.
>
> It is taking long time to go through even 100 snapshots and I have 60000
> frames. eg.
>
> trajin xx.mdcrd
> radial radial_N1_H1.dat 0.1 20 :TIP.H1:LIG.N1
>
> Is there a way I could increase computation speed for calculating rdf?
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
> _______________________________________________
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jun 01 2016 - 08:00:04 PDT
