Hello,
thanks for y our answer.
I checked it . It doesn't seem 0.
here is my out file:
NSTEP = 500 TIME(PS) = 75051.000 TEMP(K) = 411.25 PRESS =
0.0
Etot = 223.3765 EKtot = 13.4843 EPtot =
209.8922
BOND = 7.9131 ANGLE = 9.6736 DIHED =
57.0823
1-4 NB = 0.3740 1-4 EEL = 411.7846 VDWAALS =
-0.7469
EELEC = -246.1626 EGB = -30.0258 RESTRAINT =
0.0000
Carlos Simmerling <carlos.simmerling.gmail.com>, 1 May 2020 Cum, 00:18
tarihinde şunu yazdı:
> 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 <elifcigdem82.gmail.com>
> wrote:
>
> > 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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> >
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Received on Fri May 01 2020 - 05:30:01 PDT
