[gmx-users] More suitable force field and water model
ramezanpour.mohsen at gmail.com
Thu Jun 19 12:23:15 CEST 2014
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
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
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
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
any suggestion is appreciated in advance
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