Hi all,
I had some doubts on the method of calculating parameters for accelerated
MD as described in the AMBER12 manual (page no.160).
1.Does the total number of atoms (taken as 16950 in the example) include
atoms belonging to water molecules also??
2.for the calculation of alphaD, only the number of protein residues goes
as an input. What if a system has other components like DNA?? Should I
include the DNA residues also??
Kindly help.
Thanks.
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Received on Mon Apr 21 2014 - 03:00:03 PDT
