[gmx-users] More suitable force field and water model

Dr. Vitaly Chaban vvchaban at gmail.com
Fri Jun 20 11:31:05 CEST 2014

There is no best combination.

The parameters for water for your solute must be derived using
physically equivalent procedures.
That's all.

Dr. Vitaly V. Chaban

On Thu, Jun 19, 2014 at 11:59 AM, Mohsen Ramezanpour
<ramezanpour.mohsen at gmail.com> wrote:
> Dear Gromacs Users,
> I have read some articles about the more appropriate combination of force
> field and water model for different simulations of interest.
> It is confusing and too difficult to decide which combination is the best
> one. Besides according to articles I read, I am in doubt now and not sure
> which combination should I choose.
> As I understood, the SPC and TIP4P are recommended for biomolecular
> simulations and some authors have also recommended SPC.
> Although SPC/E seems the best one in non-polarizable models for bulk
> properties of water but for different quantities of interest such as
> hydration free energy, hydration enthalpy, entropy, heat capacities etc.
> some special combinations will be more appropriate.
> I found that although using a FF+water model will result in a precise
> enough quantity but we can not rely on some other quantities of our
> simulation!
> By this I mean, If we are interested in hydration free energy, the best
> option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are
> interested in other quantities as well, other combinations will be
> preferred.
> In fact I am interested in Protein-ligand binding free energy and also its
> Enthalpy and Entropy contributions as well.
> I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am
> not sure.
> I think it is also related to properties of our system components (charge,
> etc.). for example for sugars or lipids.
> Is there any article which has compared these in details? Please let me
> know.
> any suggestion is appreciated in advance
> Best Regards
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