Dear All,
I received a comment from reviewer about asking me selection of force field and water model. I choose OPLS-AAL and 3-point water model. They mentioned the combination of OPLS-AAL and SPC is stange. It looks like for OPLS-AAL, the recommend water model is tip3p. However, there is no specification on GROMACS. How do I address this?
Although the answer provided by Martin Klvana is reasonable, there is still something I would like to comment here.
First, the combination of OPLS and SPC is indeed strange. Often, we do use TIP3P or other models and SPC would not be under consideration for experienced investigators. The model has been proven to have obvious problems compared with TIP3P. I recommend you to read more papers before judging whether this is reasonable.
Second, the simulation outcome depends heavily on the force field used. Therefore, the reviewers' concern is reasonable. As you have chosen such a strange force field, your results would differ from the ones obtained with commonly used force fields. To check whether the difference would be significant, you should try to re-run your simulaiton with other force fields, or repeat your simulation to prove that your results are absolutely reproducible with your selected force field. The former re-run option is often employed in systematic investigations, while the latter could be used as a easier option when you want to address the reviewers' comments. At least, you ensure that your results are what everyone would obtain with your settings, which proves that your paper is solid and theoretically rigorous.
One last recommendation is finishing more tutorials and reading more papers before doing simulations. Otherwise, you may encounter many unexpected problems afterwards.
Reviewers often ask about force field and water model because this is a back door which is always open.
A brusque response would be that systematic errors tend to cancel out if the purpose of the simulations is to compare similar systems.
To soften the response, provide some quantitative evidence: Run a few short MD simulations with a different force field or a different water model and compare the resulting quantities (structures and energies), and show that the chosen force field [or water model] does not affect the relative quantitative results and the conclusions drawn from them.
Although the answer provided by Martin Klvana is reasonable, there is still something I would like to comment here.
First, the combination of OPLS and SPC is indeed strange. Often, we do use TIP3P or other models and SPC would not be under consideration for experienced investigators. The model has been proven to have obvious problems compared with TIP3P. I recommend you to read more papers before judging whether this is reasonable.
Second, the simulation outcome depends heavily on the force field used. Therefore, the reviewers' concern is reasonable. As you have chosen such a strange force field, your results would differ from the ones obtained with commonly used force fields. To check whether the difference would be significant, you should try to re-run your simulaiton with other force fields, or repeat your simulation to prove that your results are absolutely reproducible with your selected force field. The former re-run option is often employed in systematic investigations, while the latter could be used as a easier option when you want to address the reviewers' comments. At least, you ensure that your results are what everyone would obtain with your settings, which proves that your paper is solid and theoretically rigorous.
One last recommendation is finishing more tutorials and reading more papers before doing simulations. Otherwise, you may encounter many unexpected problems afterwards.
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