AMBER Archive (2007)

Subject: Re: AMBER: replica exchange out files continually overwritten

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Dec 14 2007 - 12:58:36 CST

Amber 10 will return to having complete output files for the entire run,
rather than being overwritten. Amber9 does overwrite due to issues with how
the
actual exchanges are done in terms of file ownership among replicas.
However, I have not seen a case with Amber9 where info files don't get
written. Also, trajectory files should NOT be overwritten, just modified
using
an append. Are you sure the traj files only have 1 frame that keeps
changing?
is nwtx less than or equal to nstlim? is ntpr less than or equal to nstlim?
both of these things work a little better in amber10, but for now make sure
that you are actually telling sander to write at least once per exchange.
carlos

On Dec 14, 2007 1:47 PM, David Mobley <dmobley_at_gmail.com> wrote:

> All,
>
> I neglected to mention that my info files are not being written. And
> everything else except rem.log and the trajectory files is being
> overwritten every iteration.
>
> Thanks,
> David
>
>
> In fact, EVERYTHING except the
>
> On Dec 14, 2007 9:17 AM, David A. Case <case_at_scripps.edu> wrote:
> > On Fri, Dec 14, 2007, David Mobley wrote:
> > >
> > > I've used AMBER 9 quite a bit, but am just trying to run my first
> > > replica exchange simulations. I appear to have MPI working properly
> > > and the simulations are running just fine. This is on a xeon cluster.
> > >
> > > However, all of my output files for individual replicas (with the
> > > exception of the trajectories) are apparently being overwritten every
> > > exchange attempt. I briefly see contents in them in between exchange
> > > attempts, for example:
> >
> > >
> > > Energy files appear to only have one block of energies ever. However,
> > > my rem.log file fills up just fine, as do my trajectory files.
> >
> > This is what you should expect. See the first paragraph in Section
> 6.9.2, p.
> > 164 of the Users' Manual: the usual roles of mdout and mdinfo are
> switched,
> > as explained there.
> >
> > Others with more Amber 9 remd experience can of course chime in here.
> >
> > ...dac
> >
> >
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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