Re: [gmx-users] replica exchange with GROMACS

[David de Sancho]

Hi
If I may answer your question, you are missing the name of your run input
file, which should be inside each of these directories. So in case you have
the set of tpr files and they are clalled run.tpr in the correct location,
adding -s run.tpr to the command should do the trick. You can find more
instructions here
http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html
All the best,

David

On Wed, 20 Nov 2019 at 16:35, hind ahmed  wrote:

>
> Hello
> Could you please direct me to how  can I run job of  replica exchange
> with GROMACS.  I used the setting bellow to submit the job on HEC, the job
> works but with no replex exchange and i got the note below.
> #run the md
> Mpirun -np 16 mdrun_mpi_d -multidir rep_0 rep_1 rep_2  rep_3  rep_4
> rep_5  rep_6  rep_7  rep_8  rep_9  rep_10 rep_11 rep_12 rep_13  rep_14
> rep_15 -replex 100
> Is there any guide to how i run it right?
>
> NOTE: The number of threads is not equal to the number of (logical) cores
>
>   and the -pin option is set to auto: will not pin thread to cores.
>   This can lead to significant performance degradation.
>   Consider using -pin on (and -pinoffset in case you run multiple
> jobs).
>
>
> Tthanks
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-- 
David De Sancho 
Ramón y Cajal Fellow (UPV/EHU)
Donostia International Physics Center
Manuel Lardizabal Ibilbidea, 4
20018 San Sebastian, Spain
Tel: +34 943018527
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[gmx-users] replica exchange with GROMACS

[hind ahmed]

Hello
Could you please direct me to how  can I run job of  replica exchange  with 
GROMACS.  I used the setting bellow to submit the job on HEC, the job works but 
with no replex exchange and i got the note below.
#run the md
Mpirun -np 16 mdrun_mpi_d -multidir rep_0 rep_1 rep_2  rep_3  rep_4  rep_5  
rep_6  rep_7  rep_8  rep_9  rep_10 rep_11 rep_12 rep_13  rep_14 rep_15 -replex 
100
Is there any guide to how i run it right?

NOTE: The number of threads is not equal to the number of (logical) cores

  and the -pin option is set to auto: will not pin thread to cores.
  This can lead to significant performance degradation.
  Consider using -pin on (and -pinoffset in case you run multiple jobs).


Tthanks
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