Ok. I will check it. Thank you so much for your answer again.
Carlos Simmerling <carlos.simmerling.gmail.com>, 1 May 2020 Cum, 15:26
tarihinde şunu yazdı:
> check your shake setting in the input (or the output, if you did not set
> it). use the manual to see details for that flag.
>
> On Fri, May 1, 2020 at 8:23 AM Elif Çiğdem Calvin <elifcigdem82.gmail.com>
> wrote:
>
> > 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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Received on Fri May 01 2020 - 05:30:03 PDT
