[AMBER] SHAKE ALgorithm and frcmod file

From: Elif Çiğdem Calvin <elifcigdem82.gmail.com>
Date: Fri, 1 May 2020 00:14:10 +0300

I parameterized a novel molecule and I sent it as an article to a journal.
TOday an interesting question came from a referee. He said :
"According to the manuscript, they employed the SHAKE algorithm in order to
apply bond constrains. This is very important and must be stated explicitly
in the manuscript since this algorithm maintains the bonds (all or some of
them? please state it) to a fixed length. As a result, the bonded
contribution to the total energy in Eq 1 (Eq 1 is the functional form of
the AMBER force field : E = Total(E-bonds) + Total(E-angles) +Total
(E-dihedral) + Total (E-LennardJones) ) becomes zero by construction and
the coefficients for the bonds in Table 1 ( Table 1 is the frcmod file that
contains bond parameters) for the bond stiffness become obsolete. I do not
imply that this approach is erroneous, it is OK but this must be stated in
the article."

Actually in the manuscript, I just mendtioned I used SHAKE Algorithm and I
didn't say in the manuscript "... we used SHAKE in order to apply bond
constrains".. But this is not important I am wondering is he right? When I
use SHAKE, does the bonded contribution to the total energy become zero?
Or what is he/she talking about? Do you have any idea?
Thank you
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Received on Thu Apr 30 2020 - 14:30:03 PDT
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