[AMBER] Regarding SHAKE Parameter

From: Sumon Naskar <205030041.iitb.ac.in>
Date: Fri, 23 Jul 2021 16:08:01 +0530

Dear All,

           I am working on a DNA-protein system. According to the
protocol, SHAKE should be applied to H containing bonds from heating
onwards. The protocol did not mention anything about the minimization in
particular. My doubt is if, in the 2 minimization stages, we do not
apply the SHAKE (ntf=1), would it really change the system as a whole? I
completed the production as well and the geometry was fine till the end.
There is one minimization with restraints on the biomolecules and one
with no restraints at all. Does not applying shake in minimization make
the simulation go wrong? What is the general purpose of applying the
SHAKE algorithm?


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Received on Fri Jul 23 2021 - 04:00:02 PDT
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