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
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====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Thu Aug 16 2012 - 12:00:02 PDT
