What version of cpptraj are you using. If not at least version 16 you
should upgrade.
-Dan
On Wed, Jun 1, 2016 at 9:58 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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
> _______________________________________________
> 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)
_______________________________________________
AMBER mailing list
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Received on Thu Jun 02 2016 - 09:00:02 PDT
