AMBER Archive (2007)

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

From: David Mobley (dmobley_at_gmail.com)
Date: Fri Dec 14 2007 - 12:47:27 CST

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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