From: mariano spivak (mariano_at_ks.uiuc.edu)
Date: Fri Aug 02 2019 - 10:01:38 CDT
Hi, I believe that the problem is that the command that you want is not
"namd".
Try in the terminal: which namd
If it does not find the command, then you might want to try "namd2" instead.
Otherwise you should find where NAMD is installed and write the full path
in the mpirun call.
Best
Mariano Spivak, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois.
On Fri, Aug 2, 2019 at 8:29 AM Adupa Vasista <adupavasista_at_gmail.com> wrote:
> Dear NAMD users
>
> I am learning replica-exchange umbrella sampling MD. I am using the
> tutorial files. I copied umbrella.namd file into my working directory.
>
> Tutorial says to use the command "mpirun -np 4 namd +replicas 4 job0.conf
> +stdout output/%d/job0.%d.log"
>
> But when i execute it the error is as follows :
>
> -------------------------------------------------------------------------------------------------------
> mpirun was unable to find the specified executable file, and therefore
> did not launch the job. This error was first reported for process
> rank 0; it may have occurred for other processes as well.
>
> NOTE: A common cause for this error is misspelling a mpirun command
> line parameter option (remember that mpirun interprets the first
> unrecognized command line token as the executable).
>
> Node: vasi
> Executable: namd
>
> -----------------------------------------------------------------------------------------------------------
>
> job0.conf file details are as follows :
>
> ------------------------------------------------------------------------------------------------------------
> source stretch_alanin.conf
>
> # prevent VMD from reading umbrella.namd by trying command only NAMD has
> if { ! [catch numPes] } { source ./umbrella.namd }
>
> ------------------------------------------------------------------------------------------------------------
>
> Can anyone point out the mistake I am making?
>
> Thank You in advance.
>
>
>
>
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