[AMBER] meaning of "tolerance" in REMD

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Wed, 15 Aug 2012 14:12:48 -0400

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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Received on Wed Aug 15 2012 - 12:00:07 PDT
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