Hi Dan,
I compiled cpptraj.OMP but I get this error:
---------- RUN BEGIN -------------------------------------------------
Error: Only 'ensemble' mode supported in parallel.
How do I specify my trajectories (which are not REMD based) as input to
ensemble?
Regards,
Neha
On 2 June 2016 at 00:42, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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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Received on Wed Jun 01 2016 - 21:00:03 PDT
