The files are certainly accessible. Let me give you a rundown of the behavior I've seen so far.
Let's say the executable is in /path.to.sander. I also a made a copy of sander.MPI in my current directory. The executables are identical.
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
Output: Unit 5 Error on OPEN: trajene.in
2)./sander.MPI -O -i trajene.in -o trajene.out -p prmtop -c inpcrd -x mdcrd.out -y mdcrd -ref inpcrd -inf trajeneinfo -r trajenerestrt
Output: None. The mdcrd.out file is correctly created.
3) I made a copy of trajene.in in /path.to.sander/sander.MPI. I then ran the same command as in (1).
Output: Unit 8 Error on OPEN: prmtop
(3) proves that /path.to/sander.MPI is expecting to find trajene.in in /path.to.sander.
Any ideas on what the problem could be?
Thanks
Ganesh Krishna
--- 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, 12:37 AM
On Sat, Apr 17, 2010, Ganesh Krishnan wrote:
> 6) It seems like sander is now refusing to accept relative paths. The
> previous version that I have, accepts relative paths without a
> problem. This one takes the location of the sander.MPI executable as the
> path to look for the mdin and other files.
This is not true. I think you need to look for other causes of the problem.
Are you sure that all nodes of your cluster see the needed files?
....dac
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Received on Sun Apr 18 2010 - 10:30:02 PDT
