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
> > _______________________________________________
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> > 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
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Received on Thu Aug 16 2012 - 15:00:03 PDT
