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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> >
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Received on Fri May 01 2020 - 05:30:02 PDT
