Hi Pratul & Daniel,
You are fast!
In fact we tried to use the "hbond" option.
We have the version 18 and the command line is:
_____________________
cpptraj.MPI complex_mr.top << EOF
trajin prod1.nc 1 last 1
trajin prod2.nc 1 last 1
autoimage
hbond :1-272 dist 3.4 angle 140.0 avgout avg_hb.dat printatomnum out vstime_hb nointramol \
solvout solvent_avg.dat bridgeout bridge.dat \
solventacceptor :WAT.O solventdonor :WAT \
series uuseries uuhbonds.agr uvseries uvhbonds.agr \
go
EOF
_____________________
.Marta, please could you give more information?
Thank you,
Dany
-----Message d'origine-----
De : Pratul Agarwal <pratul.agarwal-lab.org>
Envoyé : mardi 23 avril 2019 14:59
À : AMBER Mailing List <amber.ambermd.org>
Objet : Re: [AMBER] Issue with cpptraj.MPI
[EXTERNE]
My mistake. Please ignore "md.out" file comment. I assume you are not seeing output to any files, but what about initialization message?
Could you share your script? Also do you have a large data set?
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
-----Message d'origine-----
De : Daniel Roe <.com daniel.r.roe.gmail >
Envoyé : mardi 23 avril 2019 14:53
À : AMBER Mailing List <amber.ambermd.org>
Objet : Re: [AMBER] Issue with cpptraj.MPI
[EXTERNE]
Hi,
What version of cpptraj are you running? What is the exact command line you are executing and what does your input file look like?
-Dan
-----Message d'origine-----
De : Pratul Agarwal <pratul.agarwal-lab.org>
Envoyé : mardi 23 avril 2019 14:52
À : AMBER Mailing List <amber.ambermd.org>
Objet : Re: [AMBER] Issue with cpptraj.MPI
[EXTERNE]
Could you please give additional information? Did you see any output at all in md.out file? How do you know the program is running? Are CPUs under load?
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 4/23/2019 8:44 AM, Benard, Dany wrote:
Hi Amber Team,
We have an issue with the cpptraj.MPI command line.
We tried to run calculations on parallel CPU, the program seems running but nothing happens, no result no error message...
Did you have already see this error before?
Thank in advance for your help we are completly stuck.
Best regards,
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Received on Tue Apr 23 2019 - 06:30:02 PDT
