I admit to being a little confused by your email. You say that you didn't
use salt, and didn't think you needed to do so, but the reviewer response
makes it sound like you made claims related to salt effects in the
manuscript ("this is not a proof of the influence of salt..."). It doesn't
sound quite like the reviewer brought up salt and ions even though you
never discussed it anywhere in the manuscript - but I could be wrong, I'm
guessing without more info.
(1) I agree with Jason, that your question is about science, not really
technical questions about Amber. If you want to know how to implement the
salt, then you might ask here.
(2) if you did want feedback on the reviewer comments, you would need to
give someone the text to which the reviewer refers. without that it's
impossible to interpret the reviewer comments, because their validity
depends on what claims you made in your manuscript. In order to get helpful
suggestions, you would give your manuscript AND the reviewer comments to
someone that you trust that has relevant experience.
note that I am NOT suggesting that you follow up by sending the information
to the Amber list. As Jason said, this probably isn't the place for such
discussions. I'm just making a suggestion for what info you'll want to
share with the person you ask for help.
On Tue, Mar 1, 2016 at 8:07 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> > On Mar 1, 2016, at 1:45 AM, zahra khatti <zkhatti2000.yahoo.com> wrote:
> >
> > Dear amber usersWe investigatedthe behavior of carboplatin drugs
> inserted in boron nitride nanotubes as atransporter for use in drug
> delivery by molecular dynamics simulation using Amber12 and as amanuscript
> submitted to journal. In our case the molecules are neutral without charged
> groups, and we do not intend to investigate the ion effect. Therefore,no
> ion was added to the solvent. But the reviewer insists that forgottenion in
> solvent can dramatically cause changed in the behavior of molecule orother
> molecule in the simulations and the dynamic of the water as well.
>
> Well this is true.
>
> > Reviewer comment: “this is not a proof of the influence ofthe salt on
> all of these results, since no salt concentration was used.Performing
> theoretical investigation with precise data needs to approach arealistic
> simulation system, which represents at best the experimental world.
>
> I also agree with this. Just because you don't wish to study the effects
> of salt doesn't mean that the ions have no effect.
>
> > In this confined state where hydrophobicity is high, the dynamics of
> water andion are essential and can perturbed locally and non locally all
> the analysesdata. Rich literature exists on ion specific effects on the
> structure anddynamics of water molecules, encompassing both local and
> non-local effect. Themain results of these studies converge on the
> importance of the presence ofdissolved salts (ions) in water that leads to
> considerable changes in thedipolar correlations. Of course, the changes are
> proportional to the saltconcentration but also dependant of the salt
> species and concentrationdependent. Based on these remarks, authors should
> start again all theirsimulations, analysis and conclusion, including ions
> in the solvent.”
> >
> > I have arequest for the response to the reviewer.
>
> You need to come up with responses to the reviewer (and your professor can
> help). That's not our job. I personally think the reviewer comments are
> justified and reasonable and that you should rerun the simulations with
> some ions that correspond to realistic ionic strengths in standard
> experiments you wish to compare to.
>
> HTH,
> Jason
>
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Received on Tue Mar 01 2016 - 05:30:05 PST
