AMBER Archive (2007)

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

From: David Mobley (dmobley_at_gmail.com)
Date: Fri Dec 14 2007 - 17:04:50 CST

Carlos,

> sorry I didn't see the input earlier, last day of class syndrome.
> as I suspected, ntpr is 5000 and nstlim is 500, so you're never writing
> to the info file. we now handle this in Amber10, but in 9 you need to
> be careful since it does exactly what you ask it to do, and each exchange
> is a separate sander run so the step counter is reset.

Whoops, thanks. My bad. And you asked me about ntpr and I wrote back
giving you nstlim, ntwx, and ntwe. How useless on my part!

Thanks very much for your help.

David

> carlos
>
>
>
> On Dec 14, 2007 2:18 PM, David Mobley < dmobley_at_gmail.com> wrote:
> >
> >
> >
> > All,
> >
> >
> > > 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.
> >
> > Hmm, that sounds good.
> >
> >
> > > 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?
> >
> > Sorry this wasn't clear. My trajectory files and rem.log are the ONLY
> > files that I get complete. Everything else gets overwritten or not
> > written. So yes, I am getting trajectory files. But no info files.
> >
> >
> > > 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.
> >
> > I have nstlim = 500, ntwx = 500, ntwe = 500.
> >
> > I can send my input file again if that would be helpful. (In fact, I
> > can send a tarball of everything if you want to try reproducing it).
> >
> > Thanks,
> > David
> >
> >
> >
> >
> >
> >
> >
> >
> > >
> > >
> > >
> > >
> > > 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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> >
> > The AMBER Mail Reflector
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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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