On Sun, Apr 18, 2010 at 3:02 PM, Ganesh Krishnan <hereisganesh.yahoo.com>wrote:
> Using mpirun cleared it up. I was able to run the trajene example without a
> problem. I am still having trouble with my system though. I generated
> trajectories with and without PBC, but sander always quits by saying:
>
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
>
> It doesn't give any other information. I am assuming that the inpcrd file
> is really a placeholder when the imin=5 option is used and it doesn't care
> what I have in there. Is this correct?
>
>
correct- but it does need to have the right # atoms
> The parallel and the serial version work for the trajene example, but I am
> unable to get it working with my trajectory. Here is what I did:
>
> 1) I used a non-pbc prmtop
> 2) I have a pbc and non-pbc version of my trajectory
> 3) I couldn't get either one working with the serial or parallel version
> (called using mpirun) of sander
>
>
the prmtop and traj file need to match exactly. same # atoms, same PBC.
this means if you didn't change the traj file, use the same prmtop as what
generated the trajectory. if you modified the trajectory (stripping atoms,
etc) then you need to modify the prmtop to match exactly.
If the traj file has PBC, then the prmtop needs it too.
so, if you need more help, please be very specific about how you generated
the trajectory and prmtop.
> Here are my input files:
>
> Non-pbc version:
> minimize trajectory
> &cntrl
> imin=5, irest=0, ntx=1
> ntxo=1, cut=15.0,
> ntpr=1, ntwx=1, ntwe=1,
> nsnb=20, maxcyc=1, ncyc=1000,
> /
>
> Pbc version:
> minimize trajectory
> &cntrl
> imin=5, irest=0, ntx=5, ntb=1
> ntxo=1, cut=15.0,
> ntpr=1, ntwx=1, ntwe=1,
> nsnb=20, maxcyc=1, ncyc=1000,
> /
>
> Thanks a lot for all your help.
>
> -Ganesh Krishnan
>
> --- On Sun, 4/18/10, David A. Case <case.biomaps.rutgers.edu> wrote:
>
> From: David A. Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Trajectory Smoothing
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Sunday, April 18, 2010, 11:19 AM
>
> On Sun, Apr 18, 2010, Ganesh Krishnan wrote:
> >
> > 1) /path.to.sander/sander.MPI -O -i trajene.in -o trajene.out -p prmtop
> > -c inpcrd -x mdcrd.out -y mdcrd -ref inpcrd -inf trajeneinfo -r
> > trajenerestrt
>
> This is incorrect. You need to use mpirun for sander.MPI, e.g.
>
> mpirun -np 2 /path.to.sander/sander.MPI ....
>
> Also, the imin=5 (-y) stuff has had problems with parallel (although
> nothing
> like what you report). Does everything work OK with the serial version?
>
> Maybe this will help(?)....dac
>
>
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Received on Sun Apr 18 2010 - 13:00:02 PDT
