I finally got it working. Thanks a lot for all your help. In case anybody reads the thread in future, here is the procedure:
1) Compile sander.MPI/sander (amber9) after applying bugfix 43
2) Even though it seems counterintuitive, the inpcrd file must be valid. If it is not, sander will keep bombing
3) I got it working for PBC. I was not able to get it working for non-PBC. Probably some mistake I was making. Sander kept saying it was not able to find box info. I only need the PBC, so I am not troubleshooting further.
4) Enjoy the results of your labor
-Ganesh Krishnan
--- On Sun, 4/18/10, Ganesh Krishnan <hereisganesh.yahoo.com> wrote:
From: Ganesh Krishnan <hereisganesh.yahoo.com>
Subject: Re: [AMBER] Trajectory Smoothing
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Sunday, April 18, 2010, 12:02 PM
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?
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
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 - 13:00:04 PDT
