Hi,
I completed my thesis and I used sander program for minimization, heating
and md simulation. Today, one of jury member asked me via e-mail:
1) What is the integration algorithm is it velocity, Verlet or leap-frog?
*Actually I used SHAKE algorithm and according to my knowledge the SHAKE
is a verlet algorithm (amber uses velocity-verlet algorithm and it conserve
energy well in NVE simulations). but I am not sure. Am I wrong?
2) For sander program I referred to AMBER from here :
https://ambermd.org/CiteAmber.php
My Reference was
"D.A. Case, et. al , AMBER 2018, University of California, 923s. San
Francisco.
but the jury asked me to show another reference for only sander program.
They think amber and sander are different things. Actually I knew sander
and/or pmemd is amber itself :) But after jury's question I am not sure
anymore. Should I use another reference for sander?
Thank you
Erdem
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Received on Mon Apr 13 2020 - 09:30:02 PDT
