For pmemd you have to generate only one prmtop containing both states. But then you run the simulation just like a straight MD run. You would have to be more specific as to what exactly is failing.
I understand that this can be very confusing and I am certainly also open to any hints where the tutorial fails to explain properly.
________________________________________
From: Timothy Christopher Schutt [tschutt.mymail.mines.edu]
Sent: 04 September 2015 18:10
To: AMBER Mailing List
Subject: Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd.
Thank you for the replies! I can get it to work with Sander however still
failing with pmemd. I have been going through the tutorials and am still
confused for now but I'll keep trying, Thanks for the help!
-Tim
On Fri, Sep 4, 2015 at 12:38 AM, <hannes.loeffler.stfc.ac.uk> wrote:
> You may also want to look into tutorial A9 to see how to run TI with
> sander and pmemd but also to learn about the different ways of setup. The
> programs are quite different in this. See
> http://ambermd.org/tutorials/advanced/tutorial9/
>
> ________________________________________
> From: Timothy Christopher Schutt [tschutt.mymail.mines.edu]
> Sent: 03 September 2015 23:04
> To: amber.ambermd.org
> Subject: [AMBER] Trouble running Thermodynamic Integration in Amber14
> with pmemd.
>
> Hello all,
>
> I could really use some help. I've recently installed Amber14 and have
> been trying to get TI to run on my machine but I keep getting an error
> before it even tries to execute the simulation.
>
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> setup_groups: MPI size is not a multiple of -ng
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
> even though I'm calling for:
>
> ~/Amber14/amber14/bin/mpirun -np 2 ~/Amber14/amber14/bin/pmemd.MPI -ng 2
> -groupfile TI.groupfile
>
> I've attempted all sorts of different values for -np as well as tried
> redoing the make install for mpi with no change in result. What am I doing
> wrong? Thanks in advance for any help!
>
> -Tim
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Received on Fri Sep 04 2015 - 10:30:04 PDT
