Re: [AMBER] SHAKE ALgorithm and frcmod file

From: Carlos Simmerling <>
Date: Thu, 30 Apr 2020 17:18:27 -0400

The reviewer may be correct depending on your setting for shake. You can
check for yourself in the MD output - are your bond energies zero?

On Thu, Apr 30, 2020, 5:14 PM Elif Çiğdem Calvin <>

> Hi,
> 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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