I mean running the following command :
*mpirun -np 2 pmemd.MPI -O -i equil_1.in <
http://equil_1.in/> -o
equil_1.out -p var_3.prmtop -c var_3.inpcrd -r var_equil_3.restart*
*takes time *
*so when cpptraj runs , it simply says var_equil_3.restart is not found.*
*Actually we want to automate this by scripting so , i need the ways to
avoid this.*
*IF I manually runs the scripts , everything works fine.*
*But how do i automate ?*
*Is there any way in scripting to wait while simulation is being run and
var_equil_3.restrst is completely written and then cpptraj should run.*
*P.S. i need to submit it in the nodes on the cluster. So, there is waiting
time at times.*
*TIA!*
On Wed, Jun 16, 2021 at 6:16 PM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Jun 16, 2021, ankita mehta wrote:
>
> >*system "cpptraj -i cpptraj_3.in <http://cpptraj_3.in/>";*
>
> It's hard to know what the exact command was that you used, since something
> (your mail program, you yourself?) added the http part. Did you get any
> error messages? Is the http part really there?
>
> >*So cpptraj command doesn’t run .*
>
> Just saying "doesn't run" is very vague, and doesn't allow anyone to offer
> help. Did you get any error messages? What happens if you run the cpptraj
> command at the console (i.e. without the perl part)?
>
> ....dac
>
>
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Received on Thu Jun 17 2021 - 20:30:02 PDT
