[gmx-users] Making Commands Non-Interactive

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 5 02:42:20 CEST 2009

Justin A. Lemkul wrote:
> ABEL Stephane 175950 wrote:
>> Dear GMX Users,
>> I ask this question in this mailing list since probably a user have 
>> already
>> encountered this similar problem. I would like to  post-process my 
>> trajectory
>> with the command trjconv (in mpi mode). For this I use the following 
>> shell
>> command:
> Is trjconv parallelizable?  This is nowhere in the documentation, but if 
> it is, that would be very interesting...

No. There are no 4.0.x tools that use MPI. Hence the wiki advice not to 
bother compiling tools in parallel, and the old website installation 
guide directing the use of only "make mdrun" after reconfiguring with 

>> echo 0 | /usr/pbs/bin/mpiexec 
>> /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s
>> Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o
>> ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0
>> ("System")
>> It works but since my simulations is very long (> 300ns) the command 
>> stops in
>> the middle of the trajectory before to finish the process ( i suspect 
>> a time
>> limit for using the interactive mode). So i would like to use a script 
>> to do
>> the task. How to pass the choice 0 in the script (i.e. equivalent to 
>> the echo
>> 0). I use a bash shell and the command qsub to launch a mpi job.
>> I have tried to adapt the examples available in the GMX website with a 
>> text
>> file as suggested by the author in GROMACS site with no success.
> I routinely use a text file for scripted jobs.  Odd that yours isn't 
> working. Is it just that the command still exits before finishing?  In 
> any case, you can make an .ndx file with only an entry for [System].  
> When presented with one choice, trjconv has to choose it.

Recompiling without mpi, and doing non-mdrun operations on your local 
machine / cluster login node is usually the approach simplest to use. 
Yes, it's more work when you configure and compile, but you only do that 
every once in a while right?


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