To add on here, tolerance doesn't even have a well-defined meaning in the
scope of Amber --- there's SHAKE tolerance, QM and QM/MM tolerance (for the
SCF convergence), and minimization tolerance, just to name a few. (The one
from Amber you were quoting I think is SHAKE tolerance). None of these
make sense to appear on a T-REMD generator website, yet the first two could
easily be present in REMD simulations. And Brian was right in that the
website you cited contained references to consult for the information you
wanted (and explicitly asserted connections to Gromacs and OPLS).
He was trying to save you time by pointing you to more relevant resources
so you didn't keep asking your question to an audience that was not as well
equipped to answer (which is why, as Neil pointed out, you didn't receive
an answer the first time).
All the best,
Jason
On Thu, Aug 16, 2012 at 5:46 PM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
> The reason no one is answering your question is that "tolerance"
> doesn't have a general meaning with respect to REMD (as far as I
> know). If you would have done what Brian said, ie follow the
> references, you would see this statement in the publication:
>
> "The difference between Pdes and the probability predicted by
> the algorithm, Ppred, is used as convergence criterion with a
> tolerance that can be set interactively on the webserver, but
> typically 10-4 is good enough."
>
> This has nothing to do with bond lengths, I don't think.
> --Niel
> ________________________________________
> From: Sajeewa Pemasinghe [sajeewasp.gmail.com]
> Sent: Thursday, August 16, 2012 3:38 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Fwd: meaning of "tolerance" in REMD
>
> Hi Brian,
>
> What I wanted to know was the meaning of "tolerance" IN GENERAL with
> respect to the REMD technique. If you can give me some idea without
> directing me to another link, it would save me a lot of time(I have already
> spent some time on this, I just wanted to get my notion confirmed or
> improved by a more knowledgeable person like you ).
>
> Thank you
>
> Sajeewa Dewage
>
>
> On Thu, Aug 16, 2012 at 2:53 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > I am confused, the link you give is for a program that is not part of the
> > AMBER suite and calibrated to GROMACS results. Why did you ask the
> question
> > here?
> >
> > Also, at the bottom of that page there is ample documentation on where to
> > seek references and even the statement "In case of questions please mail
> to
> > t-remd [at] xray.bmc.uu.se"
> >
> >
> > On Thu, Aug 16, 2012 at 2:02 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> > >wrote:
> >
> > > ---------- Forwarded message ----------
> > > From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
> > > Date: Wed, Aug 15, 2012 at 2:12 PM
> > > Subject: meaning of "tolerance" in REMD
> > > To: AMBER Mailing List <amber.ambermd.org>
> > >
> > >
> > > Hi all,
> > >
> > > Could someone please correct me if I am wrong with the following
> > > interpretation of "tolerance" in REMD (I am using
> > > http://folding.bmc.uu.se/remd/index.php to generate my REMD
> > temeperatures)
> > >
> > > Tolerance in REMD refers to
> > >
> > > "The upperbound in the change of bond lengths in any two successive
> > > snapshots. So if there is a greater change in bond lengths the program
> > will
> > > give an error because it exceeds the accepted upperbound
> (i.e.tolerance).
> > > If I am using a lower time step I can use a lower tolerance"
> > >
> > > Am I correct with the above statement. Please correct me if I am wrong.
> > >
> > > Thank you (expecting a quick reply to go forward with my simulation)
> > >
> > > Sajeewa Dewage
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 16 2012 - 16:00:02 PDT
