> 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 - 05:30:03 PST
