From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Thu Jul 22 2010 - 11:29:19 CDT
Dear NAMD users,
I am using NAMD to run MD simulation on a DNA system. To the best of my knowledge, in order to check if the minimization is OK, the gradient tolerance should be checked until it drops below 1.0.
I cannot find the "gradient tolerance" in my output file. The only thing I found is
"LINE MINIMIZER REDUCING GRADIENT FROM # TO #" in which # are two different numbers.
1. Can this information be used to find the "gradient tolerance"?
2. Is "gradient tolerance" the difference between these two numbers?
3. Is this the only item that should be checked to evaluate whether the number of steps are enough for minimization?
I really appreciate your help in advance,
Parisa
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